1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 2170 2171 2172 2173 2174 2175 2176 2177 2178 2179 2180 2181 2182 2183 2184 2185 2186 2187 2188 2189 2190 2191 2192 2193 2194 2195 2196 2197 2198 2199 2200 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216 2217 2218 2219 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 2233 2234 2235 2236 2237 2238 2239 2240 2241 2242 2243 2244 2245 2246 2247 2248 2249 2250 2251 2252 2253 2254 2255 2256 2257 2258 2259 2260 2261 2262 2263 2264 2265 2266 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 2278 2279 2280 2281 2282 2283 2284 2285 2286 2287 2288 2289 2290 2291 2292 2293 2294 2295 2296 2297 2298 2299 2300 2301 2302 2303 2304 2305 2306 2307 2308 2309 2310 2311 2312 2313 2314 2315 2316 2317 2318 2319 2320 2321 2322 2323 2324 2325 2326 2327 2328 2329 2330 2331 2332 2333 2334 2335 2336 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2349 2350 2351 2352 2353 2354 2355 2356 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370 2371 2372 2373 2374 2375 2376 2377 2378 2379 2380 2381 2382 2383 2384 2385 2386 2387 2388 2389 2390 2391 2392 2393 2394 2395 2396 2397 2398 2399 2400 2401 2402 2403 2404 2405 2406 2407 2408 2409 2410 2411 2412 2413 2414 2415 2416 2417 2418 2419 2420 2421 2422 2423 2424 2425 2426 2427 2428 2429 2430 2431 2432 2433 2434 2435 2436 2437 2438 2439 2440 2441 2442 2443 2444 2445 2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460 2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674 2675 2676 2677 2678 2679 2680 2681 2682 2683 2684 2685 2686 2687 2688 2689 2690 2691 2692 2693 2694 2695 2696 2697 2698 2699 2700 2701 2702 2703 2704 2705 2706 2707 2708 2709 2710 2711 2712 2713 2714 2715 2716 2717 2718 2719 2720 2721 2722 2723 2724 2725 2726 2727 2728 2729 2730 2731 2732 2733 2734 2735 2736 2737 2738 2739 2740 2741 2742 2743 2744 2745 2746 2747 2748 2749 2750 2751 2752 2753 2754 2755 2756 2757 2758 2759 2760 2761 2762 2763 2764 2765 2766 2767 2768 2769 2770 2771 2772 2773 2774 2775 2776 2777 2778 2779 2780 2781 2782 2783 2784 2785 2786 2787 2788 2789 2790 2791 2792 2793 2794 2795 2796 2797 2798 2799 2800 2801 2802 2803 2804 2805 2806 2807 2808 2809 2810 2811 2812 2813 2814 2815 2816 2817 2818 2819 2820 2821 2822 2823 2824 2825 2826 2827 2828 2829 2830 2831 2832 2833 2834 2835 2836 2837 2838 2839 2840 2841 2842 2843 2844 2845 2846 2847 2848 2849 2850 2851 2852 2853 2854 2855 2856 2857 2858 2859 2860 2861 2862 2863 2864 2865 2866 2867 2868 2869 2870 2871 2872 2873 2874 2875 2876 2877 2878 2879 2880 2881 2882 2883 2884 2885 2886 2887 2888 2889 2890 2891 2892 2893 2894 2895 2896 2897 2898 2899 2900 2901 2902 2903 2904 2905 2906 2907 2908 2909 2910 2911 2912 2913 2914 2915 2916 2917 2918 2919 2920 2921 2922 2923 2924 2925 2926 2927 2928 2929 2930 2931 2932 2933 2934 2935 2936 2937 2938 2939 2940 2941 2942 2943 2944 2945 2946 2947 2948 2949 2950 2951 2952 2953 2954 2955 2956 2957 2958 2959 2960 2961 2962 2963 2964 2965 2966 2967 2968 2969 2970 2971 2972 2973 2974 2975 2976 2977 2978 2979 2980 2981 2982 2983 2984 2985 2986 2987 2988 2989 2990 2991 2992 2993 2994 2995 2996 2997 2998 2999 3000 3001 3002 3003 3004 3005 3006 3007 3008 3009 3010 3011 3012 3013 3014 3015 3016 3017 3018 3019 3020 3021 3022 3023 3024 3025 3026 3027 3028 3029 3030 3031 3032 3033 3034 3035 3036 3037 3038 3039 3040 3041 3042 3043 3044 3045 3046 3047 3048 3049 3050 3051 3052 3053 3054 3055 3056 3057 3058 3059 3060 3061 3062 3063
|
/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ALN_SINK_H_
#define ALN_SINK_H_
#include <limits>
#include "read.h"
#include "unique.h"
#include "sam.h"
#include "ds.h"
#include "simple_func.h"
#include "outq.h"
#include <utility>
#include "alt.h"
#include "splice_site.h"
// Forward decl
template <typename index_t>
class SeedResults;
enum {
OUTPUT_SAM = 1
};
/**
* Metrics summarizing the work done by the reporter and summarizing
* the number of reads that align, that fail to align, and that align
* non-uniquely.
*/
struct ReportingMetrics {
ReportingMetrics():mutex_m() {
reset();
}
void reset() {
init(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
}
void init(
uint64_t nread_,
uint64_t npaired_,
uint64_t nunpaired_,
uint64_t nconcord_uni_,
uint64_t nconcord_uni1_,
uint64_t nconcord_uni2_,
uint64_t nconcord_rep_,
uint64_t nconcord_0_,
uint64_t ndiscord_,
uint64_t nunp_0_uni_,
uint64_t nunp_0_uni1_,
uint64_t nunp_0_uni2_,
uint64_t nunp_0_rep_,
uint64_t nunp_0_0_,
uint64_t nunp_rep_uni_,
uint64_t nunp_rep_uni1_,
uint64_t nunp_rep_uni2_,
uint64_t nunp_rep_rep_,
uint64_t nunp_rep_0_,
uint64_t nunp_uni_,
uint64_t nunp_uni1_,
uint64_t nunp_uni2_,
uint64_t nunp_rep_,
uint64_t nunp_0_,
uint64_t sum_best1_,
uint64_t sum_best2_,
uint64_t sum_best_)
{
nread = nread_;
npaired = npaired_;
nunpaired = nunpaired_;
nconcord_uni = nconcord_uni_;
nconcord_uni1 = nconcord_uni1_;
nconcord_uni2 = nconcord_uni2_;
nconcord_rep = nconcord_rep_;
nconcord_0 = nconcord_0_;
ndiscord = ndiscord_;
nunp_0_uni = nunp_0_uni_;
nunp_0_uni1 = nunp_0_uni1_;
nunp_0_uni2 = nunp_0_uni2_;
nunp_0_rep = nunp_0_rep_;
nunp_0_0 = nunp_0_0_;
nunp_rep_uni = nunp_rep_uni_;
nunp_rep_uni1 = nunp_rep_uni1_;
nunp_rep_uni2 = nunp_rep_uni2_;
nunp_rep_rep = nunp_rep_rep_;
nunp_rep_0 = nunp_rep_0_;
nunp_uni = nunp_uni_;
nunp_uni1 = nunp_uni1_;
nunp_uni2 = nunp_uni2_;
nunp_rep = nunp_rep_;
nunp_0 = nunp_0_;
sum_best1 = sum_best1_;
sum_best2 = sum_best2_;
sum_best = sum_best_;
}
/**
* Merge (add) the counters in the given ReportingMetrics object
* into this object. This is the only safe way to update a
* ReportingMetrics shared by multiple threads.
*/
void merge(const ReportingMetrics& met, bool getLock = false) {
ThreadSafe ts(&mutex_m, getLock);
nread += met.nread;
npaired += met.npaired;
nunpaired += met.nunpaired;
nconcord_uni += met.nconcord_uni;
nconcord_uni1 += met.nconcord_uni1;
nconcord_uni2 += met.nconcord_uni2;
nconcord_rep += met.nconcord_rep;
nconcord_0 += met.nconcord_0;
ndiscord += met.ndiscord;
nunp_0_uni += met.nunp_0_uni;
nunp_0_uni1 += met.nunp_0_uni1;
nunp_0_uni2 += met.nunp_0_uni2;
nunp_0_rep += met.nunp_0_rep;
nunp_0_0 += met.nunp_0_0;
nunp_rep_uni += met.nunp_rep_uni;
nunp_rep_uni1 += met.nunp_rep_uni1;
nunp_rep_uni2 += met.nunp_rep_uni2;
nunp_rep_rep += met.nunp_rep_rep;
nunp_rep_0 += met.nunp_rep_0;
nunp_uni += met.nunp_uni;
nunp_uni1 += met.nunp_uni1;
nunp_uni2 += met.nunp_uni2;
nunp_rep += met.nunp_rep;
nunp_0 += met.nunp_0;
sum_best1 += met.sum_best1;
sum_best2 += met.sum_best2;
sum_best += met.sum_best;
}
uint64_t nread; // # reads
uint64_t npaired; // # pairs
uint64_t nunpaired; // # unpaired reads
// Paired
// Concordant
uint64_t nconcord_uni; // # pairs with unique concordant alns
uint64_t nconcord_uni1; // # pairs with exactly 1 concordant alns
uint64_t nconcord_uni2; // # pairs with >1 concordant aln, still unique
uint64_t nconcord_rep; // # pairs with repetitive concordant alns
uint64_t nconcord_0; // # pairs with 0 concordant alns
// Discordant
uint64_t ndiscord; // # pairs with 1 discordant aln
// Unpaired from failed pairs
uint64_t nunp_0_uni; // # unique from nconcord_0_ - ndiscord_
uint64_t nunp_0_uni1; // # pairs with exactly 1 concordant alns
uint64_t nunp_0_uni2; // # pairs with >1 concordant aln, still unique
uint64_t nunp_0_rep; // # repetitive from
uint64_t nunp_0_0; // # with 0 alignments
// Unpaired from repetitive pairs
uint64_t nunp_rep_uni; // # pairs with unique concordant alns
uint64_t nunp_rep_uni1; // # pairs with exactly 1 concordant alns
uint64_t nunp_rep_uni2; // # pairs with >1 concordant aln, still unique
uint64_t nunp_rep_rep; // # pairs with repetitive concordant alns
uint64_t nunp_rep_0; // # pairs with 0 concordant alns
// Unpaired
uint64_t nunp_uni; // # unique from nconcord_0_ - ndiscord_
uint64_t nunp_uni1; // # pairs with exactly 1 concordant alns
uint64_t nunp_uni2; // # pairs with >1 concordant aln, still unique
uint64_t nunp_rep; // # repetitive from
uint64_t nunp_0; // # with 0 alignments
uint64_t sum_best1; // Sum of all the best alignment scores
uint64_t sum_best2; // Sum of all the second-best alignment scores
uint64_t sum_best; // Sum of all the best and second-best
MUTEX_T mutex_m;
};
// Type for expression numbers of hits
typedef int64_t THitInt;
/**
* Parameters affecting reporting of alignments, specifically -k & -a,
* -m & -M.
*/
struct ReportingParams {
explicit ReportingParams(
THitInt khits_,
THitInt kseeds_,
THitInt mhits_,
THitInt pengap_,
bool msample_,
bool discord_,
bool mixed_)
{
init(khits_, kseeds_, mhits_, pengap_, msample_, discord_, mixed_);
}
void init(
THitInt khits_,
THitInt kseeds_,
THitInt mhits_,
THitInt pengap_,
bool msample_,
bool discord_,
bool mixed_)
{
khits = khits_; // -k (or high if -a)
kseeds = kseeds_;
mhits = ((mhits_ == 0) ? std::numeric_limits<THitInt>::max() : mhits_);
pengap = pengap_;
msample = msample_;
discord = discord_;
mixed = mixed_;
}
#ifndef NDEBUG
/**
* Check that reporting parameters are internally consistent.
*/
bool repOk() const {
assert_geq(khits, 1);
assert_geq(mhits, 1);
return true;
}
#endif
/**
* Return true iff a -m or -M limit was set by the user.
*/
inline bool mhitsSet() const {
return mhits < std::numeric_limits<THitInt>::max();
}
/**
* Return a multiplier that indicates how many alignments we might look for
* (max). We can use this to boost parameters like ROWM and POSF
* appropriately.
*/
inline THitInt mult() const {
if(mhitsSet()) {
return mhits+1;
}
return khits;
}
/**
* Given ROWM, POSF thresholds, boost them according to mult().
*/
void boostThreshold(SimpleFunc& func) {
THitInt mul = mult();
assert_gt(mul, 0);
if(mul == std::numeric_limits<THitInt>::max()) {
func.setMin(std::numeric_limits<double>::max());
} else if(mul > 1) {
func.mult(mul);
}
}
/**
* Return true iff we are reporting all hits.
*/
bool allHits() const {
return khits == std::numeric_limits<THitInt>::max();
}
// Number of alignments to report
THitInt khits;
// Number of seeds allowed to extend
THitInt kseeds;
// Read is non-unique if mhits-1 next-best alignments are within
// pengap of the best alignment
THitInt mhits, pengap;
// true if -M is specified, meaning that if the -M ceiling is
// exceeded, we should report 'khits' alignments chosen at random
// from those found
bool msample;
// true iff we should seek and report discordant paired-end alignments for
// paired-end reads.
bool discord;
// true iff we should seek and report unpaired mate alignments when there
// are paired-end alignments for a paired-end read, or if the number of
// paired-end alignments exceeds the -m ceiling.
bool mixed;
};
/**
* A state machine keeping track of the number and type of alignments found so
* far. Its purpose is to inform the caller as to what stage the alignment is
* in and what categories of alignment are still of interest. This information
* should allow the caller to short-circuit some alignment work. Another
* purpose is to tell the AlnSinkWrap how many and what type of alignment to
* report.
*
* TODO: This class does not keep accurate information about what
* short-circuiting took place. If a read is identical to a previous read,
* there should be a way to query this object to determine what work, if any,
* has to be re-done for the new read.
*/
class ReportingState {
public:
enum {
NO_READ = 1, // haven't got a read yet
CONCORDANT_PAIRS, // looking for concordant pairs
DISCORDANT_PAIRS, // looking for discordant pairs
UNPAIRED, // looking for unpaired
DONE // finished looking
};
// Flags for different ways we can finish out a category of potential
// alignments.
enum {
EXIT_DID_NOT_EXIT = 1, // haven't finished
EXIT_DID_NOT_ENTER, // never tried search
EXIT_SHORT_CIRCUIT_k, // -k exceeded
EXIT_SHORT_CIRCUIT_M, // -M exceeded
EXIT_SHORT_CIRCUIT_TRUMPED, // made irrelevant
EXIT_CONVERTED_TO_DISCORDANT, // unpair became discord
EXIT_NO_ALIGNMENTS, // none found
EXIT_WITH_ALIGNMENTS // some found
};
ReportingState(const ReportingParams& p) : p_(p) { reset(); }
/**
* Set all state to uninitialized defaults.
*/
void reset() {
state_ = ReportingState::NO_READ;
paired_ = false;
nconcord_ = 0;
ndiscord_ = 0;
nunpair1_ = 0;
nunpair2_ = 0;
doneConcord_ = false;
doneDiscord_ = false;
doneUnpair_ = false;
doneUnpair1_ = false;
doneUnpair2_ = false;
exitConcord_ = ReportingState::EXIT_DID_NOT_ENTER;
exitDiscord_ = ReportingState::EXIT_DID_NOT_ENTER;
exitUnpair1_ = ReportingState::EXIT_DID_NOT_ENTER;
exitUnpair2_ = ReportingState::EXIT_DID_NOT_ENTER;
done_ = false;
}
/**
* Return true iff this ReportingState has been initialized with a call to
* nextRead() since the last time reset() was called.
*/
bool inited() const { return state_ != ReportingState::NO_READ; }
/**
* Initialize state machine with a new read. The state we start in depends
* on whether it's paired-end or unpaired.
*/
void nextRead(bool paired);
/**
* Caller uses this member function to indicate that one additional
* concordant alignment has been found.
*/
bool foundConcordant();
/**
* Caller uses this member function to indicate that one additional
* discordant alignment has been found.
*/
bool foundUnpaired(bool mate1);
/**
* Called to indicate that the aligner has finished searching for
* alignments. This gives us a chance to finalize our state.
*
* TODO: Keep track of short-circuiting information.
*/
void finish();
/**
* Populate given counters with the number of various kinds of alignments
* to report for this read. Concordant alignments are preferable to (and
* mutually exclusive with) discordant alignments, and paired-end
* alignments are preferable to unpaired alignments.
*
* The caller also needs some additional information for the case where a
* pair or unpaired read aligns repetitively. If the read is paired-end
* and the paired-end has repetitive concordant alignments, that should be
* reported, and 'pairMax' is set to true to indicate this. If the read is
* paired-end, does not have any conordant alignments, but does have
* repetitive alignments for one or both mates, then that should be
* reported, and 'unpair1Max' and 'unpair2Max' are set accordingly.
*
* Note that it's possible in the case of a paired-end read for the read to
* have repetitive concordant alignments, but for one mate to have a unique
* unpaired alignment.
*/
void getReport(
uint64_t& nconcordAln, // # concordant alignments to report
uint64_t& ndiscordAln, // # discordant alignments to report
uint64_t& nunpair1Aln, // # unpaired alignments for mate #1 to report
uint64_t& nunpair2Aln, // # unpaired alignments for mate #2 to report
bool& pairMax, // repetitive concordant alignments
bool& unpair1Max, // repetitive alignments for mate #1
bool& unpair2Max) // repetitive alignments for mate #2
const;
/**
* Return an integer representing the alignment state we're in.
*/
inline int state() const { return state_; }
/**
* If false, there's no need to solve any more dynamic programming problems
* for finding opposite mates.
*/
inline bool doneConcordant() const { return doneConcord_; }
/**
* If false, there's no need to seek any more discordant alignment.
*/
inline bool doneDiscordant() const { return doneDiscord_; }
/**
* If false, there's no need to seek any more unpaired alignments for the
* specified mate. Note: this doesn't necessarily mean we can stop looking
* for alignments for the mate, since this might be necessary for finding
* concordant and discordant alignments.
*/
inline bool doneUnpaired(bool mate1) const {
return mate1 ? doneUnpair1_ : doneUnpair2_;
}
/**
* If false, no further consideration of the given mate is necessary. It's
* not needed for *any* class of alignment: concordant, discordant or
* unpaired.
*/
inline bool doneWithMate(bool mate1) const {
bool doneUnpair = mate1 ? doneUnpair1_ : doneUnpair2_;
uint64_t nun = mate1 ? nunpair1_ : nunpair2_;
if(!doneUnpair || !doneConcord_) {
return false; // still needed for future concordant/unpaired alns
}
if(!doneDiscord_ && nun == 0) {
return false; // still needed for future discordant alignments
}
return true; // done
}
/**
* Return true iff there's no need to seek any more unpaired alignments.
*/
inline bool doneUnpaired() const { return doneUnpair_; }
/**
* Return true iff all alignment stages have been exited.
*/
inline bool done() const { return done_; }
inline uint64_t numConcordant() const { return nconcord_; }
inline uint64_t numDiscordant() const { return ndiscord_; }
inline uint64_t numUnpaired1() const { return nunpair1_; }
inline uint64_t numUnpaired2() const { return nunpair2_; }
inline int exitConcordant() const { return exitConcord_; }
inline int exitDiscordant() const { return exitDiscord_; }
inline int exitUnpaired1() const { return exitUnpair1_; }
inline int exitUnpaired2() const { return exitUnpair2_; }
#ifndef NDEBUG
/**
* Check that ReportingState is internally consistent.
*/
bool repOk() const {
assert(p_.discord || doneDiscord_);
assert(p_.mixed || !paired_ || doneUnpair_);
assert(doneUnpair_ || !doneUnpair1_ || !doneUnpair2_);
if(p_.mhitsSet()) {
assert_leq(numConcordant(), (uint64_t)p_.mhits+1);
assert_leq(numDiscordant(), (uint64_t)p_.mhits+1);
assert(paired_ || numUnpaired1() <= (uint64_t)p_.mhits+1);
assert(paired_ || numUnpaired2() <= (uint64_t)p_.mhits+1);
}
assert(done() || !doneWithMate(true) || !doneWithMate(false));
return true;
}
#endif
/**
* Return ReportingParams object governing this ReportingState.
*/
const ReportingParams& params() const {
return p_;
}
protected:
/**
* Update state to reflect situation after converting two unique unpaired
* alignments, one for mate 1 and one for mate 2, into a single discordant
* alignment.
*/
void convertUnpairedToDiscordant() {
assert_eq(1, numUnpaired1());
assert_eq(1, numUnpaired2());
assert_eq(0, numDiscordant());
exitUnpair1_ = exitUnpair2_ = ReportingState::EXIT_CONVERTED_TO_DISCORDANT;
nunpair1_ = nunpair2_ = 0;
ndiscord_ = 1;
assert_eq(1, numDiscordant());
}
/**
* Given the number of alignments in a category, check whether we
* short-circuited out of the category. Set the done and exit arguments to
* indicate whether and how we short-circuited.
*/
inline void areDone(
uint64_t cnt, // # alignments in category
bool& done, // out: whether we short-circuited out of category
int& exit) const; // out: if done, how we short-circuited (-k? -m? etc)
/**
* Update done_ field to reflect whether we're totally done now.
*/
inline void updateDone() {
doneUnpair_ = doneUnpair1_ && doneUnpair2_;
done_ = doneUnpair_ && doneDiscord_ && doneConcord_;
}
const ReportingParams& p_; // reporting parameters
int state_; // state we're currently in
bool paired_; // true iff read we're currently handling is paired
uint64_t nconcord_; // # concordants found so far
uint64_t ndiscord_; // # discordants found so far
uint64_t nunpair1_; // # unpaired alignments found so far for mate 1
uint64_t nunpair2_; // # unpaired alignments found so far for mate 2
bool doneConcord_; // true iff we're no longner interested in concordants
bool doneDiscord_; // true iff we're no longner interested in discordants
bool doneUnpair_; // no longner interested in unpaired alns
bool doneUnpair1_; // no longner interested in unpaired alns for mate 1
bool doneUnpair2_; // no longner interested in unpaired alns for mate 2
int exitConcord_; // flag indicating how we exited concordant state
int exitDiscord_; // flag indicating how we exited discordant state
int exitUnpair1_; // flag indicating how we exited unpaired 1 state
int exitUnpair2_; // flag indicating how we exited unpaired 2 state
bool done_; // done with all alignments
};
/**
* Global hit sink for hits from the MultiSeed aligner. Encapsulates
* all aspects of the MultiSeed aligner hitsink that are global to all
* threads. This includes aspects relating to:
*
* (a) synchronized access to the output stream
* (b) the policy to be enforced by the per-thread wrapper
*
* TODO: Implement splitting up of alignments into separate files
* according to genomic coordinate.
*/
template <typename index_t>
class AlnSink {
typedef EList<std::string> StrList;
public:
explicit AlnSink(
OutputQueue& oq,
const StrList& refnames,
bool quiet,
ALTDB<index_t>* altdb = NULL,
SpliceSiteDB* ssdb = NULL) :
oq_(oq),
refnames_(refnames),
quiet_(quiet),
altdb_(altdb),
spliceSiteDB_(ssdb)
{ }
/**
* Destroy HitSinkobject;
*/
virtual ~AlnSink() { }
/**
* Called when the AlnSink is wrapped by a new AlnSinkWrap. This helps us
* keep track of whether the main lock or any of the per-stream locks will
* be contended by multiple threads.
*/
void addWrapper() { numWrappers_++; }
/**
* Append a single hit to the given output stream. If
* synchronization is required, append() assumes the caller has
* already grabbed the appropriate lock.
*/
virtual void append(
BTString& o,
StackedAln& staln,
size_t threadId,
const Read *rd1,
const Read *rd2,
const TReadId rdid,
AlnRes *rs1,
AlnRes *rs2,
const AlnSetSumm& summ,
const SeedAlSumm& ssm1,
const SeedAlSumm& ssm2,
const AlnFlags* flags1,
const AlnFlags* flags2,
const PerReadMetrics& prm,
const Mapq& mapq,
const Scoring& sc,
bool report2) = 0;
/**
* Report a given batch of hits for the given read or read pair.
* Should be called just once per read pair. Assumes all the
* alignments are paired, split between rs1 and rs2.
*
* The caller hasn't decided which alignments get reported as primary
* or secondary; that's up to the routine. Because the caller might
* want to know this, we use the pri1 and pri2 out arguments to
* convey this.
*/
virtual void reportHits(
BTString& o, // write to this buffer
StackedAln& staln, // StackedAln to write stacked alignment
size_t threadId, // which thread am I?
const Read *rd1, // mate #1
const Read *rd2, // mate #2
const TReadId rdid, // read ID
const EList<size_t>& select1, // random subset of rd1s
const EList<size_t>* select2, // random subset of rd2s
EList<AlnRes> *rs1, // alignments for mate #1
EList<AlnRes> *rs2, // alignments for mate #2
bool maxed, // true iff -m/-M exceeded
const AlnSetSumm& summ, // summary
const SeedAlSumm& ssm1, // seed alignment summ
const SeedAlSumm& ssm2, // seed alignment summ
const AlnFlags* flags1, // flags for mate #1
const AlnFlags* flags2, // flags for mate #2
const PerReadMetrics& prm, // per-read metrics
const Mapq& mapq, // MAPQ generator
const Scoring& sc, // scoring scheme
bool getLock = true) // true iff lock held by caller
{
// There are a few scenarios:
// 1. Read is unpaired, in which case rd2 is NULL
// 2. Read is paired-end and we're reporting concordant alignments
// 3. Read is paired-end and we're reporting discordant alignments
// 4. Read is paired-end and we're reporting unpaired alignments for
// both mates
// 5. Read is paired-end and we're reporting an unpaired alignments for
// just one mate or the other
assert(rd1 != NULL || rd2 != NULL);
assert(rs1 != NULL || rs2 != NULL);
AlnFlags flagscp1, flagscp2;
if(flags1 != NULL) {
flagscp1 = *flags1;
flags1 = &flagscp1;
flagscp1.setPrimary(true);
}
if(flags2 != NULL) {
flagscp2 = *flags2;
flags2 = &flagscp2;
flagscp2.setPrimary(true);
}
if(select2 != NULL) {
// Handle case 5
assert(rd1 != NULL); assert(flags1 != NULL);
assert(rd2 != NULL); assert(flags2 != NULL);
assert_gt(select1.size(), 0);
assert_gt(select2->size(), 0);
AlnRes* r1pri = ((rs1 != NULL) ? &rs1->get(select1[0]) : NULL);
AlnRes* r2pri = ((rs2 != NULL) ? &rs2->get((*select2)[0]) : NULL);
append(o, staln, threadId, rd1, rd2, rdid, r1pri, r2pri, summ,
ssm1, ssm2, flags1, flags2, prm, mapq, sc, true);
flagscp1.setPrimary(false);
flagscp2.setPrimary(false);
for(size_t i = 1; i < select1.size(); i++) {
AlnRes* r1 = ((rs1 != NULL) ? &rs1->get(select1[i]) : NULL);
append(o, staln, threadId, rd1, rd2, rdid, r1, r2pri, summ,
ssm1, ssm2, flags1, flags2, prm, mapq, sc, false);
}
for(size_t i = 1; i < select2->size(); i++) {
AlnRes* r2 = ((rs2 != NULL) ? &rs2->get((*select2)[i]) : NULL);
append(o, staln, threadId, rd2, rd1, rdid, r2, r1pri, summ,
ssm2, ssm1, flags2, flags1, prm, mapq, sc, false);
}
} else {
// Handle cases 1-4
for(size_t i = 0; i < select1.size(); i++) {
AlnRes* r1 = ((rs1 != NULL) ? &rs1->get(select1[i]) : NULL);
AlnRes* r2 = ((rs2 != NULL) ? &rs2->get(select1[i]) : NULL);
append(o, staln, threadId, rd1, rd2, rdid, r1, r2, summ,
ssm1, ssm2, flags1, flags2, prm, mapq, sc, true);
if(flags1 != NULL) {
flagscp1.setPrimary(false);
}
if(flags2 != NULL) {
flagscp2.setPrimary(false);
}
}
}
}
/**
* Report an unaligned read. Typically we do nothing, but we might
* want to print a placeholder when output is chained.
*/
virtual void reportUnaligned(
BTString& o, // write to this string
StackedAln& staln, // StackedAln to write stacked alignment
size_t threadId, // which thread am I?
const Read *rd1, // mate #1
const Read *rd2, // mate #2
const TReadId rdid, // read ID
const AlnSetSumm& summ, // summary
const SeedAlSumm& ssm1, // seed alignment summary
const SeedAlSumm& ssm2, // seed alignment summary
const AlnFlags* flags1, // flags for mate #1
const AlnFlags* flags2, // flags for mate #2
const PerReadMetrics& prm, // per-read metrics
const Mapq& mapq, // MAPQ calculator
const Scoring& sc, // scoring scheme
bool report2, // report alns for both mates?
bool getLock = true) // true iff lock held by caller
{
append(o, staln, threadId, rd1, rd2, rdid, NULL, NULL, summ,
ssm1, ssm2, flags1, flags2, prm, mapq, sc, report2);
}
/**
* Print summary of how many reads aligned, failed to align and aligned
* repetitively. Write it to stderr. Optionally write Hadoop counter
* updates.
*/
void printAlSumm(
ostream& out,
const ReportingMetrics& met,
size_t repThresh, // threshold for uniqueness, or max if no thresh
bool discord, // looked for discordant alignments
bool mixed, // looked for unpaired alignments where paired failed?
bool newSummary, // alignment summary in a new style
bool hadoopOut); // output Hadoop counters?
/**
* Called when all alignments are complete. It is assumed that no
* synchronization is necessary.
*/
void finish(
ostream& out,
size_t repThresh,
bool discord,
bool mixed,
bool newSummary,
bool hadoopOut)
{
// Close output streams
if(!quiet_) {
printAlSumm(
out,
met_,
repThresh,
discord,
mixed,
newSummary,
hadoopOut);
}
}
#ifndef NDEBUG
/**
* Check that hit sink is internally consistent.
*/
bool repOk() const { return true; }
#endif
//
// Related to reporting seed hits
//
/**
* Given a Read and associated, filled-in SeedResults objects,
* print a record summarizing the seed hits.
*/
void reportSeedSummary(
BTString& o,
const Read& rd,
TReadId rdid,
size_t threadId,
const SeedResults<index_t>& rs,
bool getLock = true);
/**
* Given a Read, print an empty record (all 0s).
*/
void reportEmptySeedSummary(
BTString& o,
const Read& rd,
TReadId rdid,
size_t threadId,
bool getLock = true);
/**
* Append a batch of unresolved seed alignment results (i.e. seed
* alignments where all we know is the reference sequence aligned
* to and its SA range, not where it falls in the reference
* sequence) to the given output stream in Bowtie's seed-alignment
* verbose-mode format.
*/
virtual void appendSeedSummary(
BTString& o,
const Read& rd,
const TReadId rdid,
size_t seedsTried,
size_t nonzero,
size_t ranges,
size_t elts,
size_t seedsTriedFw,
size_t nonzeroFw,
size_t rangesFw,
size_t eltsFw,
size_t seedsTriedRc,
size_t nonzeroRc,
size_t rangesRc,
size_t eltsRc);
/**
* Merge given metrics in with ours by summing all individual metrics.
*/
void mergeMetrics(const ReportingMetrics& met, bool getLock = true) {
met_.merge(met, getLock);
}
/**
* Return mutable reference to the shared OutputQueue.
*/
OutputQueue& outq() {
return oq_;
}
protected:
OutputQueue& oq_; // output queue
int numWrappers_; // # threads owning a wrapper for this HitSink
const StrList& refnames_; // reference names
bool quiet_; // true -> don't print alignment stats at the end
ReportingMetrics met_; // global repository of reporting metrics
ALTDB<index_t>* altdb_;
SpliceSiteDB* spliceSiteDB_; //
};
/**
* Per-thread hit sink "wrapper" for the MultiSeed aligner. Encapsulates
* aspects of the MultiSeed aligner hit sink that are per-thread. This
* includes aspects relating to:
*
* (a) Enforcement of the reporting policy
* (b) Tallying of results
* (c) Storing of results for the previous read in case this allows us to
* short-circuit some work for the next read (i.e. if it's identical)
*
* PHASED ALIGNMENT ASSUMPTION
*
* We make some assumptions about how alignment proceeds when we try to
* short-circuit work for identical reads. Specifically, we assume that for
* each read the aligner proceeds in a series of stages (or perhaps just one
* stage). In each stage, the aligner either:
*
* (a) Finds no alignments, or
* (b) Finds some alignments and short circuits out of the stage with some
* random reporting involved (e.g. in -k and/or -M modes), or
* (c) Finds all of the alignments in the stage
*
* In the event of (a), the aligner proceeds to the next stage and keeps
* trying; we can skip the stage entirely for the next read if it's identical.
* In the event of (b), or (c), the aligner stops and does not proceed to
* further stages. In the event of (b1), if the next read is identical we
* would like to tell the aligner to start again at the beginning of the stage
* that was short-circuited.
*
* In any event, the rs1_/rs2_/rs1u_/rs2u_ fields contain the alignments found
* in the last alignment stage attempted.
*
* HANDLING REPORTING LIMITS
*
* The user can specify reporting limits, like -k (specifies number of
* alignments to report out of those found) and -M (specifies a ceiling s.t. if
* there are more alignments than the ceiling, read is called repetitive and
* best found is reported). Enforcing these limits is straightforward for
* unpaired alignments: if a new alignment causes us to exceed the -M ceiling,
* we can stop looking.
*
* The case where both paired-end and unpaired alignments are possible is
* trickier. Once we have a number of unpaired alignments that exceeds the
* ceiling, we can stop looking *for unpaired alignments* - but we can't
* necessarily stop looking for paired-end alignments, since there may yet be
* more to find. However, if the input read is not a pair, then we can stop at
* this point. If the input read is a pair and we have a number of paired
* aligments that exceeds the -M ceiling, we can stop looking.
*
* CONCORDANT & DISCORDANT, PAIRED & UNPAIRED
*
* A note on paired-end alignment: Clearly, if an input read is
* paired-end and we find either concordant or discordant paired-end
* alignments for the read, then we would like to tally and report
* those alignments as such (and not as groups of 2 unpaired
* alignments). And if we fail to find any paired-end alignments, but
* we do find some unpaired alignments for one mate or the other, then
* we should clearly tally and report those alignments as unpaired
* alignments (if the user so desires).
*
* The situation is murkier when there are no paired-end alignments,
* but there are unpaired alignments for *both* mates. In this case,
* we might want to pick out zero or more pairs of mates and classify
* those pairs as discordant paired-end alignments. And we might want
* to classify the remaining alignments as unpaired. But how do we
* pick which pairs if any to call discordant?
*
* Because the most obvious use for discordant pairs is for identifying
* large-scale variation, like rearrangements or large indels, we would
* usually like to be conservative about what we call a discordant
* alignment. If there's a good chance that one or the other of the
* two mates has a good alignment to another place on the genome, this
* compromises the evidence for the large-scale variant. For this
* reason, Bowtie 2's policy is: if there are no paired-end alignments
* and there is *exactly one alignment each* for both mates, then the
* two alignments are paired and treated as a discordant paired-end
* alignment. Otherwise, all alignments are treated as unpaired
* alignments.
*
* When both paired and unpaired alignments are discovered by the
* aligner, only the paired alignments are reported by default. This
* is sensible considering relative likelihoods: if a good paired-end
* alignment is found, it is much more likely that the placement of
* the two mates implied by that paired alignment is correct than any
* placement implied by an unpaired alignment.
*
*
*/
template <typename index_t>
class AlnSinkWrap {
public:
AlnSinkWrap(
AlnSink<index_t>& g, // AlnSink being wrapped
const ReportingParams& rp, // Parameters governing reporting
Mapq& mapq, // Mapq calculator
size_t threadId, // Thread ID
bool secondary = false, // Secondary alignments
const SpliceSiteDB* ssdb = NULL, // splice sites
uint64_t threads_rids_mindist = 0) : // synchronization
g_(g),
rp_(rp),
threadid_(threadId),
mapq_(mapq),
secondary_(secondary),
ssdb_(ssdb),
threads_rids_mindist_(threads_rids_mindist),
init_(false),
maxed1_(false), // read is pair and we maxed out mate 1 unp alns
maxed2_(false), // read is pair and we maxed out mate 2 unp alns
maxedOverall_(false), // alignments found so far exceed -m/-M ceiling
bestPair_(std::numeric_limits<TAlScore>::min()),
best2Pair_(std::numeric_limits<TAlScore>::min()),
bestUnp1_(std::numeric_limits<TAlScore>::min()),
best2Unp1_(std::numeric_limits<TAlScore>::min()),
bestUnp2_(std::numeric_limits<TAlScore>::min()),
best2Unp2_(std::numeric_limits<TAlScore>::min()),
bestSplicedPair_(0),
best2SplicedPair_(0),
bestSplicedUnp1_(0),
best2SplicedUnp1_(0),
bestSplicedUnp2_(0),
best2SplicedUnp2_(0),
rd1_(NULL), // mate 1
rd2_(NULL), // mate 2
rdid_(std::numeric_limits<TReadId>::max()), // read id
rs1_(), // mate 1 alignments for paired-end alignments
rs2_(), // mate 2 alignments for paired-end alignments
rs1u_(), // mate 1 unpaired alignments
rs2u_(), // mate 2 unpaired alignments
select1_(), // for selecting random subsets for mate 1
select2_(), // for selecting random subsets for mate 2
st_(rp) // reporting state - what's left to do?
{
assert(rp_.repOk());
}
/**
* Initialize the wrapper with a new read pair and return an
* integer >= -1 indicating which stage the aligner should start
* at. If -1 is returned, the aligner can skip the read entirely.
* at. If . Checks if the new read pair is identical to the
* previous pair. If it is, then we return the id of the first
* stage to run.
*/
int nextRead(
// One of the other of rd1, rd2 will = NULL if read is unpaired
const Read* rd1, // new mate #1
const Read* rd2, // new mate #2
TReadId rdid, // read ID for new pair
bool qualitiesMatter);// aln policy distinguishes b/t quals?
/**
* Inform global, shared AlnSink object that we're finished with
* this read. The global AlnSink is responsible for updating
* counters, creating the output record, and delivering the record
* to the appropriate output stream.
*/
void finishRead(
const SeedResults<index_t> *sr1, // seed alignment results for mate 1
const SeedResults<index_t> *sr2, // seed alignment results for mate 2
bool exhaust1, // mate 1 exhausted?
bool exhaust2, // mate 2 exhausted?
bool nfilt1, // mate 1 N-filtered?
bool nfilt2, // mate 2 N-filtered?
bool scfilt1, // mate 1 score-filtered?
bool scfilt2, // mate 2 score-filtered?
bool lenfilt1, // mate 1 length-filtered?
bool lenfilt2, // mate 2 length-filtered?
bool qcfilt1, // mate 1 qc-filtered?
bool qcfilt2, // mate 2 qc-filtered?
bool sortByScore, // prioritize alignments by score
RandomSource& rnd, // pseudo-random generator
ReportingMetrics& met, // reporting metrics
const PerReadMetrics& prm, // per-read metrics
const Scoring& sc, // scoring scheme
bool suppressSeedSummary = true,
bool suppressAlignments = false,
bool templateLenAdjustment = true);
/**
* Called by the aligner when a new unpaired or paired alignment is
* discovered in the given stage. This function checks whether the
* addition of this alignment causes the reporting policy to be
* violated (by meeting or exceeding the limits set by -k, -m, -M),
* in which case true is returned immediately and the aligner is
* short circuited. Otherwise, the alignment is tallied and false
* is returned.
*/
bool report(
int stage,
const AlnRes* rs1,
const AlnRes* rs2);
#ifndef NDEBUG
/**
* Check that hit sink wrapper is internally consistent.
*/
bool repOk() const {
assert_eq(rs2_.size(), rs1_.size());
if(rp_.mhitsSet()) {
assert_gt(rp_.mhits, 0);
assert_leq((int)rs1_.size(), rp_.mhits+1);
assert_leq((int)rs2_.size(), rp_.mhits+1);
assert(readIsPair() || (int)rs1u_.size() <= rp_.mhits+1);
assert(readIsPair() || (int)rs2u_.size() <= rp_.mhits+1);
}
if(init_) {
assert(rd1_ != NULL);
assert_neq(std::numeric_limits<TReadId>::max(), rdid_);
}
assert_eq(st_.numConcordant() + st_.numDiscordant(), rs1_.size());
//assert_eq(st_.numUnpaired1(), rs1u_.size());
//assert_eq(st_.numUnpaired2(), rs2u_.size());
assert(st_.repOk());
return true;
}
#endif
/**
* Return true iff no alignments have been reported to this wrapper
* since the last call to nextRead().
*/
bool empty() const {
return rs1_.empty() && rs1u_.empty() && rs2u_.empty();
}
/**
* Return true iff we have already encountered a number of alignments that
* exceeds the -m/-M ceiling. TODO: how does this distinguish between
* pairs and mates?
*/
bool maxed() const {
return maxedOverall_;
}
/**
* Return true if the current read is paired.
*/
bool readIsPair() const {
return rd1_ != NULL && rd2_ != NULL;
}
/**
* Return true iff nextRead() has been called since the last time
* finishRead() was called.
*/
bool inited() const { return init_; }
/**
* Return a const ref to the ReportingState object associated with the
* AlnSinkWrap.
*/
const ReportingState& state() const { return st_; }
const ReportingParams& reportingParams() { return rp_;}
/**
* Return true iff we're in -M mode.
*/
bool Mmode() const {
return rp_.mhitsSet();
}
/**
* Return true iff the policy is to report all hits.
*/
bool allHits() const {
return rp_.allHits();
}
/**
* Return true iff at least two alignments have been reported so far for an
* unpaired read or mate 1.
*/
bool hasSecondBestUnp1() const {
return best2Unp1_ != std::numeric_limits<TAlScore>::min();
}
/**
* Return true iff at least two alignments have been reported so far for
* mate 2.
*/
bool hasSecondBestUnp2() const {
return best2Unp2_ != std::numeric_limits<TAlScore>::min();
}
/**
* Return true iff at least two paired-end alignments have been reported so
* far.
*/
bool hasSecondBestPair() const {
return best2Pair_ != std::numeric_limits<TAlScore>::min();
}
/**
* Get best score observed so far for an unpaired read or mate 1.
*/
TAlScore bestUnp1() const {
return bestUnp1_;
}
/**
* Get second-best score observed so far for an unpaired read or mate 1.
*/
TAlScore secondBestUnp1() const {
return best2Unp1_;
}
/**
* Get best score observed so far for mate 2.
*/
TAlScore bestUnp2() const {
return bestUnp2_;
}
/**
* Get second-best score observed so far for mate 2.
*/
TAlScore secondBestUnp2() const {
return best2Unp2_;
}
/**
* Get best score observed so far for paired-end read.
*/
TAlScore bestPair() const {
return bestPair_;
}
/**
* Get second-best score observed so far for paired-end read.
*/
TAlScore secondBestPair() const {
return best2Pair_;
}
index_t bestSplicedPair() const {
return bestSplicedPair_;
}
index_t best2SplicedPair() const {
return best2SplicedPair_;
}
index_t bestSplicedUnp1() const {
return bestSplicedUnp1_;
}
index_t best2SplicedUnp1() const {
return best2SplicedUnp1_;
}
index_t bestSplicedUnp2() const {
return bestSplicedUnp2_;
}
index_t best2SplicedUnp2() const {
return best2SplicedUnp2_;
}
bool secondary() const {
return secondary_;
}
/**
*
*/
void getUnp1(const EList<AlnRes>*& rs) const { rs = &rs1u_; }
void getUnp2(const EList<AlnRes>*& rs) const { rs = &rs2u_; }
void getPair(const EList<AlnRes>*& rs1, const EList<AlnRes>*& rs2) const { rs1 = &rs1_; rs2 = &rs2_; }
protected:
/**
* Return true iff the read in rd1/rd2 matches the last read handled, which
* should still be in rd1_/rd2_.
*/
bool sameRead(
const Read* rd1,
const Read* rd2,
bool qualitiesMatter);
/**
* If there is a configuration of unpaired alignments that fits our
* criteria for there being one or more discordant alignments, then
* shift the discordant alignments over to the rs1_/rs2_ lists, clear the
* rs1u_/rs2u_ lists and return true. Otherwise, return false.
*/
bool prepareDiscordants();
/**
* Given that rs is already populated with alignments, consider the
* alignment policy and make random selections where necessary. E.g. if we
* found 10 alignments and the policy is -k 2 -m 20, select 2 alignments at
* random. We "select" an alignment by setting the parallel entry in the
* 'select' list to true.
*/
size_t selectAlnsToReport(
const EList<AlnRes>& rs, // alignments to select from
uint64_t num, // number of alignments to select
EList<size_t>& select, // list to put results in
RandomSource& rnd)
const;
/**
* rs1 (possibly together with rs2 if reads are paired) are populated with
* alignments. Here we prioritize them according to alignment score, and
* some randomness to break ties. Priorities are returned in the 'select'
* list.
*/
size_t selectByScore(
const EList<AlnRes>* rs1, // alignments to select from (mate 1)
const EList<AlnRes>* rs2, // alignments to select from (mate 2, or NULL)
uint64_t num, // number of alignments to select
EList<size_t>& select, // prioritized list to put results in
RandomSource& rnd)
const;
AlnSink<index_t>& g_; // global alignment sink
ReportingParams rp_; // reporting parameters: khits, mhits etc
size_t threadid_; // thread ID
Mapq& mapq_; // mapq calculator
bool secondary_; // allow for secondary alignments
const SpliceSiteDB* ssdb_; // splice sites
uint64_t threads_rids_mindist_; // synchronization
bool init_; // whether we're initialized w/ read pair
bool maxed1_; // true iff # unpaired mate-1 alns reported so far exceeded -m/-M
bool maxed2_; // true iff # unpaired mate-2 alns reported so far exceeded -m/-M
bool maxedOverall_; // true iff # paired-end alns reported so far exceeded -m/-M
TAlScore bestPair_; // greatest score so far for paired-end
TAlScore best2Pair_; // second-greatest score so far for paired-end
TAlScore bestUnp1_; // greatest score so far for unpaired/mate1
TAlScore best2Unp1_; // second-greatest score so far for unpaired/mate1
TAlScore bestUnp2_; // greatest score so far for mate 2
TAlScore best2Unp2_; // second-greatest score so far for mate 2
index_t bestSplicedPair_;
index_t best2SplicedPair_;
index_t bestSplicedUnp1_;
index_t best2SplicedUnp1_;
index_t bestSplicedUnp2_;
index_t best2SplicedUnp2_;
const Read* rd1_; // mate #1
const Read* rd2_; // mate #2
TReadId rdid_; // read ID (potentially used for ordering)
EList<AlnRes> rs1_; // paired alignments for mate #1
EList<AlnRes> rs2_; // paired alignments for mate #2
EList<AlnRes> rs1u_; // unpaired alignments for mate #1
EList<AlnRes> rs2u_; // unpaired alignments for mate #2
EList<size_t> select1_; // parallel to rs1_/rs2_ - which to report
EList<size_t> select2_; // parallel to rs1_/rs2_ - which to report
ReportingState st_; // reporting state - what's left to do?
EList<std::pair<TAlScore, size_t> > selectBuf_;
BTString obuf_;
StackedAln staln_;
EList<SpliceSite> spliceSites_;
};
/**
* An AlnSink concrete subclass for printing SAM alignments. The user might
* want to customize SAM output in various ways. We encapsulate all these
* customizations, and some of the key printing routines, in the SamConfig
* class in sam.h/sam.cpp.
*/
template <typename index_t>
class AlnSinkSam : public AlnSink<index_t> {
typedef EList<std::string> StrList;
public:
AlnSinkSam(
OutputQueue& oq, // output queue
const SamConfig<index_t>& samc, // settings & routines for SAM output
const StrList& refnames, // reference names
bool quiet, // don't print alignment summary at end
ALTDB<index_t>* altdb = NULL,
SpliceSiteDB* ssdb = NULL) :
AlnSink<index_t>(
oq,
refnames,
quiet,
altdb,
ssdb),
samc_(samc)
{ }
virtual ~AlnSinkSam() { }
/**
* Append a single alignment result, which might be paired or
* unpaired, to the given output stream in Bowtie's verbose-mode
* format. If the alignment is paired-end, print mate1's alignment
* then mate2's alignment.
*/
virtual void append(
BTString& o, // write output to this string
StackedAln& staln, // StackedAln to write stacked alignment
size_t threadId, // which thread am I?
const Read* rd1, // mate #1
const Read* rd2, // mate #2
const TReadId rdid, // read ID
AlnRes* rs1, // alignments for mate #1
AlnRes* rs2, // alignments for mate #2
const AlnSetSumm& summ, // summary
const SeedAlSumm& ssm1, // seed alignment summary
const SeedAlSumm& ssm2, // seed alignment summary
const AlnFlags* flags1, // flags for mate #1
const AlnFlags* flags2, // flags for mate #2
const PerReadMetrics& prm, // per-read metrics
const Mapq& mapq, // MAPQ calculator
const Scoring& sc, // scoring scheme
bool report2) // report alns for both mates
{
assert(rd1 != NULL || rd2 != NULL);
if(rd1 != NULL) {
assert(flags1 != NULL);
appendMate(o, staln, *rd1, rd2, rdid, rs1, rs2, summ, ssm1, ssm2,
*flags1, prm, mapq, sc);
if(rs1 != NULL && rs1->spliced() && this->spliceSiteDB_ != NULL) {
this->spliceSiteDB_->addSpliceSite(*rd1, *rs1);
}
}
if(rd2 != NULL && report2) {
assert(flags2 != NULL);
appendMate(o, staln, *rd2, rd1, rdid, rs2, rs1, summ, ssm2, ssm1,
*flags2, prm, mapq, sc);
if(rs2 != NULL && rs2->spliced() && this->spliceSiteDB_ != NULL) {
this->spliceSiteDB_->addSpliceSite(*rd2, *rs2);
}
}
}
protected:
/**
* Append a single per-mate alignment result to the given output
* stream. If the alignment is part of a pair, information about
* the opposite mate and its alignment are given in rdo/rso.
*/
void appendMate(
BTString& o,
StackedAln& staln,
const Read& rd,
const Read* rdo,
const TReadId rdid,
AlnRes* rs,
AlnRes* rso,
const AlnSetSumm& summ,
const SeedAlSumm& ssm,
const SeedAlSumm& ssmo,
const AlnFlags& flags,
const PerReadMetrics& prm, // per-read metrics
const Mapq& mapq, // MAPQ calculator
const Scoring& sc); // scoring scheme
const SamConfig<index_t>& samc_; // settings & routines for SAM output
BTDnaString dseq_; // buffer for decoded read sequence
BTString dqual_; // buffer for decoded quality sequence
};
static inline std::ostream& printPct(
std::ostream& os,
uint64_t num,
uint64_t denom)
{
double pct = 0.0f;
if(denom != 0) { pct = 100.0 * (double)num / (double)denom; }
os << fixed << setprecision(2) << pct << '%';
return os;
}
/**
* Print a friendly summary of:
*
* 1. How many reads were aligned and had one or more alignments
* reported
* 2. How many reads exceeded the -m or -M ceiling and therefore had
* their alignments suppressed or sampled
* 3. How many reads failed to align entirely
*
* Optionally print a series of Hadoop streaming-style counter updates
* with similar information.
*/
template <typename index_t>
void AlnSink<index_t>::printAlSumm(
ostream& out,
const ReportingMetrics& met,
size_t repThresh, // threshold for uniqueness, or max if no thresh
bool discord, // looked for discordant alignments
bool mixed, // looked for unpaired alignments where paired failed?
bool newSummary, // alignment summary in a new style
bool hadoopOut) // output Hadoop counters?
{
// NOTE: there's a filtering step at the very beginning, so everything
// being reported here is post filtering
bool canRep = repThresh != MAX_SIZE_T;
if(hadoopOut) {
out << "reporter:counter:HISAT2,Reads processed," << met.nread << endl;
}
uint64_t totread = met.nread;
uint64_t totpair = met.npaired;
uint64_t totunpair = met.nunpaired;
uint64_t tot_al_cand = totunpair + totpair*2;
uint64_t tot_al = (met.nconcord_uni + met.nconcord_rep) * 2 + (met.ndiscord) * 2 + met.nunp_0_uni + met.nunp_0_rep + met.nunp_uni + met.nunp_rep;
assert_leq(tot_al, tot_al_cand);
if(newSummary) {
out << "HISAT2 summary stats:" << endl;
if(totpair > 0) {
uint64_t ncondiscord_0 = met.nconcord_0 - met.ndiscord;
out << "\tTotal pairs: " << totpair << endl;
out << "\t\tAligned concordantly or discordantly 0 time: " << ncondiscord_0 << " ("; printPct(out, ncondiscord_0, met.npaired); out << ")" << endl;
out << "\t\tAligned concordantly 1 time: " << met.nconcord_uni1 << " ("; printPct(out, met.nconcord_uni1, met.npaired); out << ")" << endl;
out << "\t\tAligned concordantly >1 times: " << met.nconcord_uni2 << " ("; printPct(out, met.nconcord_uni2, met.npaired); out << ")" << endl;
out << "\t\tAligned discordantly 1 time: " << met.ndiscord << " ("; printPct(out, met.ndiscord, met.npaired); out << ")" << endl;
out << "\tTotal unpaired reads: " << ncondiscord_0 * 2 << endl;
out << "\t\tAligned 0 time: " << met.nunp_0_0 << " ("; printPct(out, met.nunp_0_0, ncondiscord_0 * 2); out << ")" << endl;
out << "\t\tAligned 1 time: " << met.nunp_0_uni1 << " ("; printPct(out, met.nunp_0_uni1, ncondiscord_0 * 2); out << ")" << endl;
out << "\t\tAligned >1 times: " << met.nunp_0_uni2 << " ("; printPct(out, met.nunp_0_uni2, ncondiscord_0 * 2); out << ")" << endl;
} else {
out << "\tTotal reads: " << totread << endl;
out << "\t\tAligned 0 time: " << met.nunp_0 << " ("; printPct(out, met.nunp_0, met.nunpaired); out << ")" << endl;
out << "\t\tAligned 1 time: " << met.nunp_uni1 << " ("; printPct(out, met.nunp_uni1, met.nunpaired); out << ")" << endl;
out << "\t\tAligned >1 times: " << met.nunp_uni2 << " ("; printPct(out, met.nunp_uni2, met.nunpaired); out << ")" << endl;
}
out << "\tOverall alignment rate: "; printPct(out, tot_al, tot_al_cand); out << endl;
} else {
if(totread > 0) {
out << "" << totread << " reads; of these:" << endl;
} else {
assert_eq(0, met.npaired);
assert_eq(0, met.nunpaired);
out << "" << totread << " reads" << endl;
}
if(totpair > 0) {
// Paired output
out << " " << totpair << " (";
printPct(out, totpair, totread);
out << ") were paired; of these:" << endl;
// Concordants
out << " " << met.nconcord_0 << " (";
printPct(out, met.nconcord_0, met.npaired);
out << ") aligned concordantly 0 times" << endl;
if(canRep) {
// Print the number that aligned concordantly exactly once
assert_eq(met.nconcord_uni, met.nconcord_uni1+met.nconcord_uni2);
out << " " << met.nconcord_uni1 << " (";
printPct(out, met.nconcord_uni1, met.npaired);
out << ") aligned concordantly exactly 1 time" << endl;
// Print the number that aligned concordantly more than once but
// fewer times than the limit
out << " " << met.nconcord_uni2+met.nconcord_rep << " (";
printPct(out, met.nconcord_uni2+met.nconcord_rep, met.npaired);
out << ") aligned concordantly >1 times" << endl;
} else {
// Print the number that aligned concordantly exactly once
assert_eq(met.nconcord_uni, met.nconcord_uni1+met.nconcord_uni2);
out << " " << met.nconcord_uni1 << " (";
printPct(out, met.nconcord_uni1, met.npaired);
out << ") aligned concordantly exactly 1 time" << endl;
// Print the number that aligned concordantly more than once
out << " " << met.nconcord_uni2 << " (";
printPct(out, met.nconcord_uni2, met.npaired);
out << ") aligned concordantly >1 times" << endl;
}
if(discord) {
// TODO: what about discoardant and on separate chromosomes?
// Bring out the unaligned pair total so we can subtract discordants
out << " ----" << endl;
out << " " << met.nconcord_0
<< " pairs aligned concordantly 0 times; of these:" << endl;
// Discordants
out << " " << met.ndiscord << " (";
printPct(out, met.ndiscord, met.nconcord_0);
out << ") aligned discordantly 1 time" << endl;
}
uint64_t ncondiscord_0 = met.nconcord_0 - met.ndiscord;
if(mixed) {
// Bring out the unaligned pair total so we can subtract discordants
out << " ----" << endl;
out << " " << ncondiscord_0
<< " pairs aligned 0 times concordantly or discordantly; of these:" << endl;
out << " " << (ncondiscord_0 * 2) << " mates make up the pairs; of these:" << endl;
out << " " << met.nunp_0_0 << " " << "(";
printPct(out, met.nunp_0_0, ncondiscord_0 * 2);
out << ") aligned 0 times" << endl;
if(canRep) {
// Print the number that aligned exactly once
assert_eq(met.nunp_0_uni, met.nunp_0_uni1+met.nunp_0_uni2);
out << " " << met.nunp_0_uni1 << " (";
printPct(out, met.nunp_0_uni1, ncondiscord_0 * 2);
out << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once but fewer times
// than the limit
out << " " << met.nunp_0_uni2+met.nunp_0_rep << " (";
printPct(out, met.nunp_0_uni2+met.nunp_0_rep, ncondiscord_0 * 2);
out << ") aligned >1 times" << endl;
} else {
// Print the number that aligned exactly once
assert_eq(met.nunp_0_uni, met.nunp_0_uni1+met.nunp_0_uni2);
out << " " << met.nunp_0_uni1 << " (";
printPct(out, met.nunp_0_uni1, ncondiscord_0 * 2);
out << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once but fewer times
// than the limit
out << " " << met.nunp_0_uni2 << " (";
printPct(out, met.nunp_0_uni2, ncondiscord_0 * 2);
out << ") aligned >1 times" << endl;
}
}
}
if(totunpair > 0) {
// Unpaired output
out << " " << totunpair << " (";
printPct(out, totunpair, totread);
out << ") were unpaired; of these:" << endl;
out << " " << met.nunp_0 << " (";
printPct(out, met.nunp_0, met.nunpaired);
out << ") aligned 0 times" << endl;
if(hadoopOut) {
out << "reporter:counter:HISAT 2,Unpaired reads with 0 alignments,"
<< met.nunpaired << endl;
}
if(canRep) {
// Print the number that aligned exactly once
assert_eq(met.nunp_uni, met.nunp_uni1+met.nunp_uni2);
out << " " << met.nunp_uni1 << " (";
printPct(out, met.nunp_uni1, met.nunpaired);
out << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once but fewer times
// than the limit
out << " " << met.nunp_uni2+met.nunp_rep << " (";
printPct(out, met.nunp_uni2+met.nunp_rep, met.nunpaired);
out << ") aligned >1 times" << endl;
} else {
// Print the number that aligned exactly once
assert_eq(met.nunp_uni, met.nunp_uni1+met.nunp_uni2);
out << " " << met.nunp_uni1 << " (";
printPct(out, met.nunp_uni1, met.nunpaired);
out << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once
out << " " << met.nunp_uni2 << " (";
printPct(out, met.nunp_uni2, met.nunpaired);
out << ") aligned >1 times" << endl;
}
}
printPct(out, tot_al, tot_al_cand);
out << " overall alignment rate" << endl;
}
}
/**
* Return true iff the read in rd1/rd2 matches the last read handled, which
* should still be in rd1_/rd2_.
*/
template <typename index_t>
bool AlnSinkWrap<index_t>::sameRead(
// One of the other of rd1, rd2 will = NULL if read is unpaired
const Read* rd1, // new mate #1
const Read* rd2, // new mate #2
bool qualitiesMatter) // aln policy distinguishes b/t quals?
{
bool same = false;
if(rd1_ != NULL || rd2_ != NULL) {
// This is not the first time the sink was initialized with
// a read. Check if new read/pair is identical to previous
// read/pair
if((rd1_ == NULL) == (rd1 == NULL) &&
(rd2_ == NULL) == (rd2 == NULL))
{
bool m1same = (rd1 == NULL && rd1_ == NULL);
if(!m1same) {
assert(rd1 != NULL);
assert(rd1_ != NULL);
m1same = Read::same(
rd1->patFw, // new seq
rd1->qual, // new quals
rd1_->patFw, // old seq
rd1_->qual, // old quals
qualitiesMatter);
}
if(m1same) {
bool m2same = (rd2 == NULL && rd2_ == NULL);
if(!m2same) {
m2same = Read::same(
rd2->patFw, // new seq
rd2->qual, // new quals
rd2_->patFw, // old seq
rd2_->qual, // old quals
qualitiesMatter);
}
same = m2same;
}
}
}
return same;
}
/**
* Initialize the wrapper with a new read pair and return an integer >= -1
* indicating which stage the aligner should start at. If -1 is returned, the
* aligner can skip the read entirely. Checks if the new read pair is
* identical to the previous pair. If it is, then we return the id of the
* first stage to run.
*/
template <typename index_t>
int AlnSinkWrap<index_t>::nextRead(
// One of the other of rd1, rd2 will = NULL if read is unpaired
const Read* rd1, // new mate #1
const Read* rd2, // new mate #2
TReadId rdid, // read ID for new pair
bool qualitiesMatter) // aln policy distinguishes b/t quals?
{
assert(!init_);
assert(rd1 != NULL || rd2 != NULL);
init_ = true;
// Keep copy of new read, so that we can compare it with the
// next one
if(rd1 != NULL) {
rd1_ = rd1;
} else rd1_ = NULL;
if(rd2 != NULL) {
rd2_ = rd2;
} else rd2_ = NULL;
rdid_ = rdid;
// Caller must now align the read
maxed1_ = false;
maxed2_ = false;
maxedOverall_ = false;
bestPair_ = best2Pair_ =
bestUnp1_ = best2Unp1_ =
bestUnp2_ = best2Unp2_ = std::numeric_limits<THitInt>::min();
bestSplicedPair_ = best2SplicedPair_ =
bestSplicedUnp1_ = best2SplicedUnp1_ =
bestSplicedUnp2_ = best2SplicedUnp2_ = 0;
rs1_.clear(); // clear out paired-end alignments
rs2_.clear(); // clear out paired-end alignments
rs1u_.clear(); // clear out unpaired alignments for mate #1
rs2u_.clear(); // clear out unpaired alignments for mate #2
st_.nextRead(readIsPair()); // reset state
assert(empty());
assert(!maxed());
// Start from the first stage
return 0;
}
/**
* Inform global, shared AlnSink object that we're finished with this read.
* The global AlnSink is responsible for updating counters, creating the output
* record, and delivering the record to the appropriate output stream.
*
* What gets reported for a paired-end alignment?
*
* 1. If there are reportable concordant alignments, report those and stop
* 2. If there are reportable discordant alignments, report those and stop
* 3. If unpaired alignments can be reported:
* 3a. Report
#
* Update metrics. Only ambiguity is: what if a pair aligns repetitively and
* one of its mates aligns uniquely?
*
* uint64_t al; // # mates w/ >= 1 reported alignment
* uint64_t unal; // # mates w/ 0 alignments
* uint64_t max; // # mates withheld for exceeding -M/-m ceiling
* uint64_t al_concord; // # pairs w/ >= 1 concordant alignment
* uint64_t al_discord; // # pairs w/ >= 1 discordant alignment
* uint64_t max_concord; // # pairs maxed out
* uint64_t unal_pair; // # pairs where neither mate aligned
*/
template <typename index_t>
void AlnSinkWrap<index_t>::finishRead(
const SeedResults<index_t> *sr1, // seed alignment results for mate 1
const SeedResults<index_t> *sr2, // seed alignment results for mate 2
bool exhaust1, // mate 1 exhausted?
bool exhaust2, // mate 2 exhausted?
bool nfilt1, // mate 1 N-filtered?
bool nfilt2, // mate 2 N-filtered?
bool scfilt1, // mate 1 score-filtered?
bool scfilt2, // mate 2 score-filtered?
bool lenfilt1, // mate 1 length-filtered?
bool lenfilt2, // mate 2 length-filtered?
bool qcfilt1, // mate 1 qc-filtered?
bool qcfilt2, // mate 2 qc-filtered?
bool sortByScore, // prioritize alignments by score
RandomSource& rnd, // pseudo-random generator
ReportingMetrics& met, // reporting metrics
const PerReadMetrics& prm, // per-read metrics
const Scoring& sc, // scoring scheme
bool suppressSeedSummary, // = true
bool suppressAlignments, // = false
bool templateLenAdjustment) // = true
{
obuf_.clear();
OutputQueueMark qqm(g_.outq(), obuf_, rdid_, threadid_);
assert(init_);
if(!suppressSeedSummary) {
if(sr1 != NULL) {
assert(rd1_ != NULL);
// Mate exists and has non-empty SeedResults
g_.reportSeedSummary(obuf_, *rd1_, rdid_, threadid_, *sr1, true);
} else if(rd1_ != NULL) {
// Mate exists but has NULL SeedResults
g_.reportEmptySeedSummary(obuf_, *rd1_, rdid_, true);
}
if(sr2 != NULL) {
assert(rd2_ != NULL);
// Mate exists and has non-empty SeedResults
g_.reportSeedSummary(obuf_, *rd2_, rdid_, threadid_, *sr2, true);
} else if(rd2_ != NULL) {
// Mate exists but has NULL SeedResults
g_.reportEmptySeedSummary(obuf_, *rd2_, rdid_, true);
}
}
if(!suppressAlignments) {
// Ask the ReportingState what to report
st_.finish();
uint64_t nconcord = 0, ndiscord = 0, nunpair1 = 0, nunpair2 = 0;
bool pairMax = false, unpair1Max = false, unpair2Max = false;
st_.getReport(
nconcord,
ndiscord,
nunpair1,
nunpair2,
pairMax,
unpair1Max,
unpair2Max);
assert_leq(nconcord, rs1_.size());
assert_leq(nunpair1, rs1u_.size());
assert_leq(nunpair2, rs2u_.size());
assert_leq(ndiscord, 1);
assert_gt(rp_.khits, 0);
assert_gt(rp_.mhits, 0);
assert(!pairMax || rs1_.size() >= (uint64_t)rp_.mhits);
assert(!unpair1Max || rs1u_.size() >= (uint64_t)rp_.mhits);
assert(!unpair2Max || rs2u_.size() >= (uint64_t)rp_.mhits);
met.nread++;
if(readIsPair()) {
met.npaired++;
} else {
met.nunpaired++;
}
// Report concordant paired-end alignments if possible
if(nconcord > 0) {
AlnSetSumm concordSumm(
rd1_, rd2_, &rs1_, &rs2_, &rs1u_, &rs2u_,
exhaust1, exhaust2, -1, -1);
// Possibly select a random subset
size_t off;
if(sortByScore) {
// Sort by score then pick from low to high
off = selectByScore(&rs1_, &rs2_, nconcord, select1_, rnd);
} else {
// Select subset randomly
off = selectAlnsToReport(rs1_, nconcord, select1_, rnd);
}
concordSumm.numAlnsPaired(select1_.size());
assert_lt(off, rs1_.size());
const AlnRes *rs1 = &rs1_[off];
const AlnRes *rs2 = &rs2_[off];
AlnFlags flags1(
ALN_FLAG_PAIR_CONCORD_MATE1,
st_.params().mhitsSet(),
unpair1Max,
pairMax,
nfilt1,
scfilt1,
lenfilt1,
qcfilt1,
st_.params().mixed,
true, // primary
true, // opp aligned
rs2->fw()); // opp fw
AlnFlags flags2(
ALN_FLAG_PAIR_CONCORD_MATE2,
st_.params().mhitsSet(),
unpair2Max,
pairMax,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
false, // primary
true, // opp aligned
rs1->fw()); // opp fw
// Issue: we only set the flags once, but some of the flags might
// vary from pair to pair among the pairs we're reporting. For
// instance, whether a given mate aligns to the forward strand.
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL && sr2 != NULL) {
sr1->toSeedAlSumm(ssm1);
sr2->toSeedAlSumm(ssm2);
}
for(size_t i = 0; i < rs1_.size(); i++) {
spliceSites_.clear();
if(templateLenAdjustment) {
rs1_[i].setMateParams(ALN_RES_TYPE_MATE1, &rs2_[i], flags1, ssdb_, threads_rids_mindist_, &spliceSites_);
rs2_[i].setMateParams(ALN_RES_TYPE_MATE2, &rs1_[i], flags2, ssdb_, threads_rids_mindist_, &spliceSites_);
} else {
rs1_[i].setMateParams(ALN_RES_TYPE_MATE1, &rs2_[i], flags1);
rs2_[i].setMateParams(ALN_RES_TYPE_MATE2, &rs1_[i], flags2);
}
assert_eq(abs(rs1_[i].fragmentLength()), abs(rs2_[i].fragmentLength()));
}
assert(!select1_.empty());
g_.reportHits(
obuf_,
staln_,
threadid_,
rd1_,
rd2_,
rdid_,
select1_,
NULL,
&rs1_,
&rs2_,
pairMax,
concordSumm,
ssm1,
ssm2,
&flags1,
&flags2,
prm,
mapq_,
sc);
if(pairMax) {
met.nconcord_rep++;
} else {
met.nconcord_uni++;
assert(!rs1_.empty());
if(select1_.size() == 1) {
met.nconcord_uni1++;
} else {
met.nconcord_uni2++;
}
}
init_ = false;
//g_.outq().finishRead(obuf_, rdid_, threadid_);
return;
}
// Report concordant paired-end alignments if possible
else if(ndiscord > 0) {
ASSERT_ONLY(bool ret =) prepareDiscordants();
assert(ret);
assert_eq(1, rs1_.size());
assert_eq(1, rs2_.size());
AlnSetSumm discordSumm(
rd1_, rd2_, &rs1_, &rs2_, &rs1u_, &rs2u_,
exhaust1, exhaust2, -1, -1);
const AlnRes *rs1 = &rs1_[0];
const AlnRes *rs2 = &rs2_[0];
AlnFlags flags1(
ALN_FLAG_PAIR_DISCORD_MATE1,
st_.params().mhitsSet(),
false,
pairMax,
nfilt1,
scfilt1,
lenfilt1,
qcfilt1,
st_.params().mixed,
true, // primary
true, // opp aligned
rs2->fw()); // opp fw
AlnFlags flags2(
ALN_FLAG_PAIR_DISCORD_MATE2,
st_.params().mhitsSet(),
false,
pairMax,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
false, // primary
true, // opp aligned
rs1->fw()); // opp fw
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
for(size_t i = 0; i < rs1_.size(); i++) {
rs1_[i].setMateParams(ALN_RES_TYPE_MATE1, &rs2_[i], flags1);
rs2_[i].setMateParams(ALN_RES_TYPE_MATE2, &rs1_[i], flags2);
assert(rs1_[i].isFraglenSet() == rs2_[i].isFraglenSet());
assert(!rs1_[i].isFraglenSet() || abs(rs1_[i].fragmentLength()) == abs(rs2_[i].fragmentLength()));
}
ASSERT_ONLY(size_t off);
if(sortByScore) {
// Sort by score then pick from low to high
ASSERT_ONLY(off =) selectByScore(&rs1_, &rs2_, ndiscord, select1_, rnd);
} else {
// Select subset randomly
ASSERT_ONLY(off =) selectAlnsToReport(rs1_, ndiscord, select1_, rnd);
}
assert_eq(0, off);
assert(!select1_.empty());
g_.reportHits(
obuf_,
staln_,
threadid_,
rd1_,
rd2_,
rdid_,
select1_,
NULL,
&rs1_,
&rs2_,
pairMax,
discordSumm,
ssm1,
ssm2,
&flags1,
&flags2,
prm,
mapq_,
sc);
met.nconcord_0++;
met.ndiscord++;
init_ = false;
//g_.outq().finishRead(obuf_, rdid_, threadid_);
return;
}
// If we're at this point, at least one mate failed to align.
// BTL: That's not true. It could be that there are no concordant
// alignments but both mates have unpaired alignments, with one of
// the mates having more than one.
//assert(nunpair1 == 0 || nunpair2 == 0);
assert(!pairMax);
const AlnRes *repRs1 = NULL, *repRs2 = NULL;
AlnSetSumm summ1, summ2;
AlnFlags flags1, flags2;
TRefId refid = -1; TRefOff refoff = -1;
bool rep1 = rd1_ != NULL && nunpair1 > 0;
bool rep2 = rd2_ != NULL && nunpair2 > 0;
// This is the preliminary if statement for mate 1 - here we're
// gathering some preliminary information, making it possible to call
// g_.reportHits(...) with information about both mates potentially
if(rep1) {
// Mate 1 aligned at least once
if(rep2) {
summ1.init(
rd1_, rd2_, NULL, NULL, &rs1u_, &rs2u_,
exhaust1, exhaust2, -1, -1);
} else {
summ1.init(
rd1_, NULL, NULL, NULL, &rs1u_, NULL,
exhaust1, exhaust2, -1, -1);
}
size_t off;
if(sortByScore) {
// Sort by score then pick from low to high
off = selectByScore(&rs1u_, NULL, nunpair1, select1_, rnd);
} else {
// Select subset randomly
off = selectAlnsToReport(rs1u_, nunpair1, select1_, rnd);
}
summ1.numAlns1(select1_.size());
summ2.numAlns1(select1_.size());
repRs1 = &rs1u_[off];
} else if(rd1_ != NULL) {
// Mate 1 failed to align - don't do anything yet. First we want
// to collect information on mate 2 in case that factors into the
// summary
assert(!unpair1Max);
}
if(rep2) {
if(rep1) {
summ2.init(
rd1_, rd2_, NULL, NULL, &rs1u_, &rs2u_,
exhaust1, exhaust2, -1, -1);
} else {
summ2.init(
NULL, rd2_, NULL, NULL, NULL, &rs2u_,
exhaust1, exhaust2, -1, -1);
}
size_t off;
if(sortByScore) {
// Sort by score then pick from low to high
off = selectByScore(&rs2u_, NULL, nunpair2, select2_, rnd);
} else {
// Select subset randomly
off = selectAlnsToReport(rs2u_, nunpair2, select2_, rnd);
}
repRs2 = &rs2u_[off];
summ1.numAlns2(select2_.size());
summ2.numAlns2(select2_.size());
} else if(rd2_ != NULL) {
// Mate 2 failed to align - don't do anything yet. First we want
// to collect information on mate 1 in case that factors into the
// summary
assert(!unpair2Max);
}
// Update counters given that one mate didn't align
if(readIsPair()) {
met.nconcord_0++;
}
if(rd1_ != NULL) {
if(nunpair1 > 0) {
// Update counters
if(readIsPair()) {
if(unpair1Max) met.nunp_0_rep++;
else {
met.nunp_0_uni++;
assert(!rs1u_.empty());
if(select1_.size() == 1) {
met.nunp_0_uni1++;
} else {
met.nunp_0_uni2++;
}
}
} else {
if(unpair1Max) met.nunp_rep++;
else {
met.nunp_uni++;
assert(!rs1u_.empty());
if(select1_.size() == 1) {
met.nunp_uni1++;
} else {
met.nunp_uni2++;
}
}
}
} else if(unpair1Max) {
// Update counters
if(readIsPair()) met.nunp_0_rep++;
else met.nunp_rep++;
} else {
// Update counters
if(readIsPair()) met.nunp_0_0++;
else met.nunp_0++;
}
}
if(rd2_ != NULL) {
if(nunpair2 > 0) {
// Update counters
if(readIsPair()) {
if(unpair2Max) met.nunp_0_rep++;
else {
assert(!rs2u_.empty());
met.nunp_0_uni++;
if(select2_.size() == 1) {
met.nunp_0_uni1++;
} else {
met.nunp_0_uni2++;
}
}
} else {
if(unpair2Max) met.nunp_rep++;
else {
assert(!rs2u_.empty());
met.nunp_uni++;
if(select2_.size() == 1) {
met.nunp_uni1++;
} else {
met.nunp_uni2++;
}
}
}
} else if(unpair2Max) {
// Update counters
if(readIsPair()) met.nunp_0_rep++;
else met.nunp_rep++;
} else {
// Update counters
if(readIsPair()) met.nunp_0_0++;
else met.nunp_0++;
}
}
// Now set up flags
if(rep1) {
// Initialize flags. Note: We want to have information about how
// the other mate aligned (if it did) at this point
flags1.init(
readIsPair() ?
ALN_FLAG_PAIR_UNPAIRED_MATE1 :
ALN_FLAG_PAIR_UNPAIRED,
st_.params().mhitsSet(),
unpair1Max,
pairMax,
nfilt1,
scfilt1,
lenfilt1,
qcfilt1,
st_.params().mixed,
true, // primary
repRs2 != NULL, // opp aligned
repRs2 == NULL || repRs2->fw()); // opp fw
for(size_t i = 0; i < rs1u_.size(); i++) {
rs1u_[i].setMateParams(ALN_RES_TYPE_UNPAIRED_MATE1, NULL, flags1);
}
}
if(rep2) {
// Initialize flags. Note: We want to have information about how
// the other mate aligned (if it did) at this point
flags2.init(
readIsPair() ?
ALN_FLAG_PAIR_UNPAIRED_MATE2 :
ALN_FLAG_PAIR_UNPAIRED,
st_.params().mhitsSet(),
unpair2Max,
pairMax,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
true, // primary
repRs1 != NULL, // opp aligned
repRs1 == NULL || repRs1->fw()); // opp fw
for(size_t i = 0; i < rs2u_.size(); i++) {
rs2u_[i].setMateParams(ALN_RES_TYPE_UNPAIRED_MATE2, NULL, flags2);
}
}
// Now report mate 1
if(rep1) {
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
assert(!select1_.empty());
g_.reportHits(
obuf_,
staln_,
threadid_,
rd1_,
repRs2 != NULL ? rd2_ : NULL,
rdid_,
select1_,
repRs2 != NULL ? &select2_ : NULL,
&rs1u_,
repRs2 != NULL ? &rs2u_ : NULL,
unpair1Max,
summ1,
ssm1,
ssm2,
&flags1,
repRs2 != NULL ? &flags2 : NULL,
prm,
mapq_,
sc);
assert_lt(select1_[0], rs1u_.size());
refid = rs1u_[select1_[0]].refid();
refoff = rs1u_[select1_[0]].refoff();
}
// Now report mate 2
if(rep2 && !rep1) {
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
assert(!select2_.empty());
g_.reportHits(
obuf_,
staln_,
threadid_,
rd2_,
repRs1 != NULL ? rd1_ : NULL,
rdid_,
select2_,
repRs1 != NULL ? &select1_ : NULL,
&rs2u_,
repRs1 != NULL ? &rs1u_ : NULL,
unpair2Max,
summ2,
ssm1,
ssm2,
&flags2,
repRs1 != NULL ? &flags1 : NULL,
prm,
mapq_,
sc);
assert_lt(select2_[0], rs2u_.size());
refid = rs2u_[select2_[0]].refid();
refoff = rs2u_[select2_[0]].refoff();
}
if(rd1_ != NULL && nunpair1 == 0) {
if(nunpair2 > 0) {
assert_neq(-1, refid);
summ1.init(
rd1_, NULL, NULL, NULL, NULL, NULL,
exhaust1, exhaust2, refid, refoff);
} else {
summ1.init(
rd1_, NULL, NULL, NULL, NULL, NULL,
exhaust1, exhaust2, -1, -1);
}
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
flags1.init(
readIsPair() ?
ALN_FLAG_PAIR_UNPAIRED_MATE1 :
ALN_FLAG_PAIR_UNPAIRED,
st_.params().mhitsSet(),
false,
false,
nfilt1,
scfilt1,
lenfilt1,
qcfilt1,
st_.params().mixed,
true, // primary
repRs2 != NULL, // opp aligned
(repRs2 != NULL) ? repRs2->fw() : false); // opp fw
g_.reportUnaligned(
obuf_, // string to write output to
staln_,
threadid_,
rd1_, // read 1
NULL, // read 2
rdid_, // read id
summ1, // summ
ssm1, //
ssm2,
&flags1, // flags 1
NULL, // flags 2
prm, // per-read metrics
mapq_, // MAPQ calculator
sc, // scoring scheme
true); // get lock?
}
if(rd2_ != NULL && nunpair2 == 0) {
if(nunpair1 > 0) {
assert_neq(-1, refid);
summ2.init(
NULL, rd2_, NULL, NULL, NULL, NULL,
exhaust1, exhaust2, refid, refoff);
} else {
summ2.init(
NULL, rd2_, NULL, NULL, NULL, NULL,
exhaust1, exhaust2, -1, -1);
}
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
flags2.init(
readIsPair() ?
ALN_FLAG_PAIR_UNPAIRED_MATE2 :
ALN_FLAG_PAIR_UNPAIRED,
st_.params().mhitsSet(),
false,
false,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
true, // primary
repRs1 != NULL, // opp aligned
(repRs1 != NULL) ? repRs1->fw() : false); // opp fw
g_.reportUnaligned(
obuf_, // string to write output to
staln_,
threadid_,
rd2_, // read 1
NULL, // read 2
rdid_, // read id
summ2, // summ
ssm1,
ssm2,
&flags2, // flags 1
NULL, // flags 2
prm, // per-read metrics
mapq_, // MAPQ calculator
sc, // scoring scheme
true); // get lock?
}
} // if(suppress alignments)
init_ = false;
return;
}
/**
* Called by the aligner when a new unpaired or paired alignment is
* discovered in the given stage. This function checks whether the
* addition of this alignment causes the reporting policy to be
* violated (by meeting or exceeding the limits set by -k, -m, -M),
* in which case true is returned immediately and the aligner is
* short circuited. Otherwise, the alignment is tallied and false
* is returned.
*/
template <typename index_t>
bool AlnSinkWrap<index_t>::report(
int stage,
const AlnRes* rs1,
const AlnRes* rs2)
{
assert(init_);
assert(rs1 != NULL || rs2 != NULL);
assert(rs1 == NULL || !rs1->empty());
assert(rs2 == NULL || !rs2->empty());
assert(rs1 == NULL || rs1->repOk());
assert(rs2 == NULL || rs2->repOk());
bool paired = (rs1 != NULL && rs2 != NULL);
bool one = (rs1 != NULL);
const AlnRes* rsa = one ? rs1 : rs2;
const AlnRes* rsb = one ? rs2 : rs1;
if(paired) {
assert(readIsPair());
st_.foundConcordant();
rs1_.push_back(*rs1);
rs2_.push_back(*rs2);
} else {
st_.foundUnpaired(one);
if(one) {
rs1u_.push_back(*rs1);
} else {
rs2u_.push_back(*rs2);
}
}
// Tally overall alignment score
TAlScore score = rsa->score().score();
if(rsb != NULL) score += rsb->score().score();
index_t num_spliced = (index_t)rsa->num_spliced();
if(rsb != NULL) num_spliced += (index_t)rsb->num_spliced();
// Update best score so far
if(paired) {
if(score > bestPair_) {
best2Pair_ = bestPair_;
bestPair_ = score;
best2SplicedPair_ = bestSplicedPair_;
bestSplicedPair_ = num_spliced;
} else if(score > best2Pair_) {
best2Pair_ = score;
best2SplicedPair_ = num_spliced;
}
} else {
if(one) {
if(score > bestUnp1_) {
best2Unp1_ = bestUnp1_;
bestUnp1_ = score;
best2SplicedUnp1_ = bestSplicedUnp1_;
bestSplicedUnp1_ = num_spliced;
} else if(score > best2Unp1_) {
best2Unp1_ = score;
best2SplicedUnp1_ = num_spliced;
}
} else {
if(score > bestUnp2_) {
best2Unp2_ = bestUnp2_;
bestUnp2_ = score;
best2SplicedUnp2_ = bestSplicedUnp2_;
bestSplicedUnp2_ = num_spliced;
} else if(score > best2Unp2_) {
best2Unp2_ = score;
best2SplicedUnp1_ = num_spliced;
}
}
}
return st_.done();
}
/**
* If there is a configuration of unpaired alignments that fits our
* criteria for there being one or more discordant alignments, then
* shift the discordant alignments over to the rs1_/rs2_ lists, clear the
* rs1u_/rs2u_ lists and return true. Otherwise, return false.
*/
template <typename index_t>
bool AlnSinkWrap<index_t>::prepareDiscordants() {
if(rs1u_.size() == 1 && rs2u_.size() == 1) {
assert(rs1_.empty());
assert(rs2_.empty());
rs1_.push_back(rs1u_[0]);
rs2_.push_back(rs2u_[0]);
return true;
}
return false;
}
/**
* rs1 (possibly together with rs2 if reads are paired) are populated with
* alignments. Here we prioritize them according to alignment score, and
* some randomness to break ties. Priorities are returned in the 'select'
* list.
*/
template <typename index_t>
size_t AlnSinkWrap<index_t>::selectByScore(
const EList<AlnRes>* rs1, // alignments to select from (mate 1)
const EList<AlnRes>* rs2, // alignments to select from (mate 2, or NULL)
uint64_t num, // number of alignments to select
EList<size_t>& select, // prioritized list to put results in
RandomSource& rnd)
const
{
assert(init_);
assert(repOk());
assert_gt(num, 0);
assert(rs1 != NULL);
size_t sz = rs1->size(); // sz = # alignments found
assert_leq(num, sz);
if(sz < num) {
num = sz;
}
// num = # to select
if(sz < 1) {
return 0;
}
select.resize((size_t)num);
// Use 'selectBuf_' as a temporary list for sorting purposes
EList<std::pair<TAlScore, size_t> >& buf =
const_cast<EList<std::pair<TAlScore, size_t> >& >(selectBuf_);
buf.resize(sz);
// Sort by score. If reads are pairs, sort by sum of mate scores.
for(size_t i = 0; i < sz; i++) {
buf[i].first = (*rs1)[i].score().hisat2_score();
if(rs2 != NULL) {
buf[i].first += (*rs2)[i].score().hisat2_score();
}
buf[i].second = i; // original offset
}
buf.sort(); buf.reverse(); // sort in descending order by score
// Randomize streaks of alignments that are equal by score
size_t streak = 0;
for(size_t i = 1; i < buf.size(); i++) {
if(buf[i].first == buf[i-1].first) {
if(streak == 0) { streak = 1; }
streak++;
} else {
if(streak > 1) {
assert_geq(i, streak);
buf.shufflePortion(i-streak, streak, rnd);
}
streak = 0;
}
}
if(streak > 1) {
buf.shufflePortion(buf.size() - streak, streak, rnd);
}
for(size_t i = 0; i < num; i++) { select[i] = buf[i].second; }
if(!secondary_) {
assert_geq(buf.size(), select.size());
for(size_t i = 0; i + 1 < select.size(); i++) {
if(buf[i].first != buf[i+1].first) {
select.resize(i+1);
break;
}
}
}
// Returns index of the representative alignment, but in 'select' also
// returns the indexes of the next best selected alignments in order by
// score.
return selectBuf_[0].second;
}
/**
* Given that rs is already populated with alignments, consider the
* alignment policy and make random selections where necessary. E.g. if we
* found 10 alignments and the policy is -k 2 -m 20, select 2 alignments at
* random. We "select" an alignment by setting the parallel entry in the
* 'select' list to true.
*
* Return the "representative" alignment. This is simply the first one
* selected. That will also be what SAM calls the "primary" alignment.
*/
template <typename index_t>
size_t AlnSinkWrap<index_t>::selectAlnsToReport(
const EList<AlnRes>& rs, // alignments to select from
uint64_t num, // number of alignments to select
EList<size_t>& select, // list to put results in
RandomSource& rnd)
const
{
assert(init_);
assert(repOk());
assert_gt(num, 0);
size_t sz = rs.size();
if(sz < num) {
num = sz;
}
if(sz < 1) {
return 0;
}
select.resize((size_t)num);
if(sz == 1) {
assert_eq(1, num);
select[0] = 0;
return 0;
}
// Select a random offset into the list of alignments
uint32_t off = rnd.nextU32() % (uint32_t)sz;
uint32_t offOrig = off;
// Now take elements starting at that offset, wrapping around to 0 if
// necessary. Leave the rest.
for(size_t i = 0; i < num; i++) {
select[i] = off;
off++;
if(off == sz) {
off = 0;
}
}
return offOrig;
}
#define NOT_SUPPRESSED !suppress_[field++]
#define BEGIN_FIELD { \
if(firstfield) firstfield = false; \
else o.append('\t'); \
}
#define WRITE_TAB { \
if(firstfield) firstfield = false; \
else o.append('\t'); \
}
#define WRITE_NUM(o, x) { \
itoa10(x, buf); \
o.append(buf); \
}
/**
* Print a seed summary to the first output stream in the outs_ list.
*/
template <typename index_t>
void AlnSink<index_t>::reportSeedSummary(
BTString& o,
const Read& rd,
TReadId rdid,
size_t threadId,
const SeedResults<index_t>& rs,
bool getLock)
{
appendSeedSummary(
o, // string to write to
rd, // read
rdid, // read id
rs.numOffs()*2, // # seeds tried
rs.nonzeroOffsets(), // # seeds with non-empty results
rs.numRanges(), // # ranges for all seed hits
rs.numElts(), // # elements for all seed hits
rs.numOffs(), // # seeds tried from fw read
rs.nonzeroOffsetsFw(), // # seeds with non-empty results from fw read
rs.numRangesFw(), // # ranges for seed hits from fw read
rs.numEltsFw(), // # elements for seed hits from fw read
rs.numOffs(), // # seeds tried from rc read
rs.nonzeroOffsetsRc(), // # seeds with non-empty results from fw read
rs.numRangesRc(), // # ranges for seed hits from fw read
rs.numEltsRc()); // # elements for seed hits from fw read
}
/**
* Print an empty seed summary to the first output stream in the outs_ list.
*/
template <typename index_t>
void AlnSink<index_t>::reportEmptySeedSummary(
BTString& o,
const Read& rd,
TReadId rdid,
size_t threadId,
bool getLock)
{
appendSeedSummary(
o, // string to append to
rd, // read
rdid, // read id
0, // # seeds tried
0, // # seeds with non-empty results
0, // # ranges for all seed hits
0, // # elements for all seed hits
0, // # seeds tried from fw read
0, // # seeds with non-empty results from fw read
0, // # ranges for seed hits from fw read
0, // # elements for seed hits from fw read
0, // # seeds tried from rc read
0, // # seeds with non-empty results from fw read
0, // # ranges for seed hits from fw read
0); // # elements for seed hits from fw read
}
/**
* Print the given string. If ws = true, print only up to and not
* including the first space or tab. Useful for printing reference
* names.
*/
template<typename T>
static inline void printUptoWs(
BTString& s,
const T& str,
bool chopws)
{
size_t len = str.length();
for(size_t i = 0; i < len; i++) {
if(!chopws || (str[i] != ' ' && str[i] != '\t')) {
s.append(str[i]);
} else {
break;
}
}
}
/**
* Append a batch of unresolved seed alignment summary results (i.e.
* seed alignments where all we know is the reference sequence aligned
* to and its SA range, not where it falls in the reference
* sequence) to the given output stream in Bowtie's seed-sumamry
* verbose-mode format.
*
* The seed summary format is:
*
* - One line per read
* - A typical line consists of a set of tab-delimited fields:
*
* 1. Read name
* 2. Total number of seeds extracted from the read
* 3. Total number of seeds that aligned to the reference at
* least once (always <= field 2)
* 4. Total number of distinct BW ranges found in all seed hits
* (always >= field 3)
* 5. Total number of distinct BW elements found in all seed
* hits (always >= field 4)
* 6-9.: Like 2-5. but just for seeds extracted from the
* forward representation of the read
* 10-13.: Like 2-5. but just for seeds extracted from the
* reverse-complement representation of the read
*
* Note that fields 6 and 10 should add to field 2, 7 and 11
* should add to 3, etc.
*
* - Lines for reads that are filtered out for any reason (e.g. too
* many Ns) have columns 2 through 13 set to 0.
*/
template <typename index_t>
void AlnSink<index_t>::appendSeedSummary(
BTString& o,
const Read& rd,
const TReadId rdid,
size_t seedsTried,
size_t nonzero,
size_t ranges,
size_t elts,
size_t seedsTriedFw,
size_t nonzeroFw,
size_t rangesFw,
size_t eltsFw,
size_t seedsTriedRc,
size_t nonzeroRc,
size_t rangesRc,
size_t eltsRc)
{
char buf[1024];
bool firstfield = true;
//
// Read name
//
BEGIN_FIELD;
printUptoWs(o, rd.name, true);
//
// Total number of seeds tried
//
BEGIN_FIELD;
WRITE_NUM(o, seedsTried);
//
// Total number of seeds tried where at least one range was found.
//
BEGIN_FIELD;
WRITE_NUM(o, nonzero);
//
// Total number of ranges found
//
BEGIN_FIELD;
WRITE_NUM(o, ranges);
//
// Total number of elements found
//
BEGIN_FIELD;
WRITE_NUM(o, elts);
//
// The same four numbers, but only for seeds extracted from the
// forward read representation.
//
BEGIN_FIELD;
WRITE_NUM(o, seedsTriedFw);
BEGIN_FIELD;
WRITE_NUM(o, nonzeroFw);
BEGIN_FIELD;
WRITE_NUM(o, rangesFw);
BEGIN_FIELD;
WRITE_NUM(o, eltsFw);
//
// The same four numbers, but only for seeds extracted from the
// reverse complement read representation.
//
BEGIN_FIELD;
WRITE_NUM(o, seedsTriedRc);
BEGIN_FIELD;
WRITE_NUM(o, nonzeroRc);
BEGIN_FIELD;
WRITE_NUM(o, rangesRc);
BEGIN_FIELD;
WRITE_NUM(o, eltsRc);
o.append('\n');
}
/**
* Append a single hit to the given output stream in Bowtie's
* verbose-mode format.
*/
template <typename index_t>
void AlnSinkSam<index_t>::appendMate(
BTString& o, // append to this string
StackedAln& staln, // store stacked alignment struct here
const Read& rd,
const Read* rdo,
const TReadId rdid,
AlnRes* rs,
AlnRes* rso,
const AlnSetSumm& summ,
const SeedAlSumm& ssm,
const SeedAlSumm& ssmo,
const AlnFlags& flags,
const PerReadMetrics& prm,
const Mapq& mapqCalc,
const Scoring& sc)
{
if(rs == NULL && samc_.omitUnalignedReads()) {
return;
}
char buf[1024];
char mapqInps[1024];
if(rs != NULL) {
staln.reset();
rs->initStacked(rd, staln);
staln.leftAlign(false /* not past MMs */);
}
int offAdj = 0;
// QNAME
samc_.printReadName(o, rd.name, flags.partOfPair());
o.append('\t');
// FLAG
int fl = 0;
if(flags.partOfPair()) {
fl |= SAM_FLAG_PAIRED;
if(flags.alignedConcordant()) {
fl |= SAM_FLAG_MAPPED_PAIRED;
}
if(!flags.mateAligned()) {
// Other fragment is unmapped
fl |= SAM_FLAG_MATE_UNMAPPED;
}
fl |= (flags.readMate1() ?
SAM_FLAG_FIRST_IN_PAIR : SAM_FLAG_SECOND_IN_PAIR);
if(flags.mateAligned() && rso != NULL) {
if(!rso->fw()) {
fl |= SAM_FLAG_MATE_STRAND;
}
}
}
if(!flags.isPrimary()) {
fl |= SAM_FLAG_NOT_PRIMARY;
}
if(rs != NULL && !rs->fw()) {
fl |= SAM_FLAG_QUERY_STRAND;
}
if(rs == NULL) {
// Failed to align
fl |= SAM_FLAG_UNMAPPED;
}
itoa10<int>(fl, buf);
o.append(buf);
o.append('\t');
// RNAME
if(rs != NULL) {
samc_.printRefNameFromIndex(o, (size_t)rs->refid());
o.append('\t');
} else {
if(summ.orefid() != -1) {
// Opposite mate aligned but this one didn't - print the opposite
// mate's RNAME and POS as is customary
assert(flags.partOfPair());
samc_.printRefNameFromIndex(o, (size_t)summ.orefid());
} else {
// No alignment
o.append('*');
}
o.append('\t');
}
// POS
// Note: POS is *after* soft clipping. I.e. POS points to the
// upstream-most character *involved in the clipped alignment*.
if(rs != NULL) {
itoa10<int64_t>(rs->refoff()+1+offAdj, buf);
o.append(buf);
o.append('\t');
} else {
if(summ.orefid() != -1) {
// Opposite mate aligned but this one didn't - print the opposite
// mate's RNAME and POS as is customary
assert(flags.partOfPair());
itoa10<int64_t>(summ.orefoff()+1+offAdj, buf);
o.append(buf);
} else {
// No alignment
o.append('0');
}
o.append('\t');
}
// MAPQ
mapqInps[0] = '\0';
if(rs != NULL) {
itoa10<TMapq>(mapqCalc.mapq(
summ, flags, rd.mate < 2, rd.length(),
rdo == NULL ? 0 : rdo->length(), mapqInps), buf);
o.append(buf);
o.append('\t');
} else {
// No alignment
o.append("0\t");
}
// CIGAR
if(rs != NULL) {
staln.buildCigar(false);
staln.writeCigar(&o, NULL);
o.append('\t');
} else {
// No alignment
o.append("*\t");
}
// RNEXT
if(rs != NULL && flags.partOfPair()) {
if(rso != NULL && rs->refid() != rso->refid()) {
samc_.printRefNameFromIndex(o, (size_t)rso->refid());
o.append('\t');
} else {
o.append("=\t");
}
} else if(summ.orefid() != -1) {
// The convention if this mate fails to align but the other doesn't is
// to copy the mate's details into here
o.append("=\t");
} else {
o.append("*\t");
}
// PNEXT
if(rs != NULL && flags.partOfPair()) {
if(rso != NULL) {
itoa10<int64_t>(rso->refoff()+1, buf);
o.append(buf);
o.append('\t');
} else {
// The convenstion is that if this mate aligns but the opposite
// doesn't, we print this mate's offset here
itoa10<int64_t>(rs->refoff()+1, buf);
o.append(buf);
o.append('\t');
}
} else if(summ.orefid() != -1) {
// The convention if this mate fails to align but the other doesn't is
// to copy the mate's details into here
itoa10<int64_t>(summ.orefoff()+1, buf);
o.append(buf);
o.append('\t');
} else {
o.append("0\t");
}
// ISIZE
if(rs != NULL && rs->isFraglenSet()) {
itoa10<int64_t>(rs->fragmentLength(), buf);
o.append(buf);
o.append('\t');
} else {
// No fragment
o.append("0\t");
}
// SEQ
if(!flags.isPrimary() && samc_.omitSecondarySeqQual()) {
o.append('*');
} else {
// Print the read
if(rd.patFw.length() == 0) {
o.append('*');
} else {
if(rs == NULL || rs->fw()) {
o.append(rd.patFw.toZBuf());
} else {
o.append(rd.patRc.toZBuf());
}
}
}
o.append('\t');
// QUAL
if(!flags.isPrimary() && samc_.omitSecondarySeqQual()) {
o.append('*');
} else {
// Print the quals
if(rd.qual.length() == 0) {
o.append('*');
} else {
if(rs == NULL || rs->fw()) {
o.append(rd.qual.toZBuf());
} else {
o.append(rd.qualRev.toZBuf());
}
}
}
o.append('\t');
//
// Optional fields
//
if(rs != NULL) {
samc_.printAlignedOptFlags(
o, // output buffer
true, // first opt flag printed is first overall?
rd, // read
*rs, // individual alignment result
staln, // stacked alignment
flags, // alignment flags
summ, // summary of alignments for this read
ssm, // seed alignment summary
prm, // per-read metrics
sc, // scoring scheme
mapqInps, // inputs to MAPQ calculation
this->altdb_);
} else {
samc_.printEmptyOptFlags(
o, // output buffer
true, // first opt flag printed is first overall?
rd, // read
flags, // alignment flags
summ, // summary of alignments for this read
ssm, // seed alignment summary
prm, // per-read metrics
sc); // scoring scheme
}
o.append('\n');
}
#endif /*ndef ALN_SINK_H_*/
|