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package align2;
import java.io.File;
import java.util.BitSet;
import java.util.Locale;
import fileIO.FileFormat;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import shared.Parse;
import shared.PreParser;
import shared.Tools;
import stream.Header;
import stream.Read;
import stream.SamLine;
public class GradeSamFile {
public static void main(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
args=pp.args;
//outstream=pp.outstream;
}
String in=null, outl=null, outs=null;
long reads=-1;
for(int i=0; i<args.length; i++){
final String arg=args[i];
final String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(a.equals("in") || a.equals("in1")){
in=b;
}else if(a.equals("reads")){
reads=Parse.parseKMG(b);
}else if(a.equals("parsecustom")){
parsecustom=Parse.parseBoolean(b);
}else if(a.equals("thresh")){
THRESH2=Integer.parseInt(b);
}else if(a.equals("printerr")){
printerr=Parse.parseBoolean(b);
// }else if(a.equals("ssaha2") || a.equals("subtractleadingclip")){
// SamLine.SUBTRACT_LEADING_SOFT_CLIP=Parse.parseBoolean(b);
}else if(a.equals("blasr")){
BLASR=Parse.parseBoolean(b);
}else if(a.equals("q") || a.equals("quality") || a.startsWith("minq")){
minQuality=Integer.parseInt(b);
}else if(a.equals("bitset")){
USE_BITSET=Parse.parseBoolean(b);
}else if(a.equals("outloose") || a.equals("outl")){
outl=b;
}else if(a.equals("outstrict") || a.equals("outs")){
outs=b;
}else if(i==0 && args[i].indexOf('=')<0 && (a.startsWith("stdin") || new File(args[0]).exists())){
in=args[0];
}else if(i==1 && args[i].indexOf('=')<0 && Tools.isDigit(a.charAt(0))){
reads=Parse.parseKMG(a);
}else{
throw new RuntimeException("Unknown parameter "+arg);
}
}
if(outl!=null){
ffLoose=FileFormat.testOutput(outl, FileFormat.SAM, null, false, true, false, false);
tswLoose=new TextStreamWriter(ffLoose);
tswLoose.start();
}
if(outs!=null){
ffStrict=FileFormat.testOutput(outs, FileFormat.SAM, null, false, true, false, false);
tswStrict=new TextStreamWriter(ffStrict);
tswStrict.start();
}
if(USE_BITSET){
int x=400000;
if(reads>0 && reads<=Integer.MAX_VALUE){x=(int)reads;}
try {
seen=new BitSet(x);
} catch (Throwable e) {
seen=null;
e.printStackTrace();
System.out.println("Did not have enough memory to allocate bitset; duplicate mappings will not be detected.");
}
}
assert(in!=null) : args[0]+".exists() ? "+new File(args[0]).exists();
if(reads<1){
assert(false) : "Number of expected reads was not specified. Please add a parameter reads=<number> or disable assertions.";
System.err.println("Warning - number of expected reads was not specified.");
}
TextFile tf=new TextFile(in, false);
String s=null;
for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
char c=s.charAt(0);
// System.out.println(s);
if(c!='@'/* && c!=' ' && c!='\t'*/){
SamLine sl=new SamLine(s);
lines++;
int id=(parsecustom && seen!=null ? ((((int)sl.parseNumericId())<<1)|sl.pairnum()) : (int)lines);
// System.out.println(sl.parseNumericId()+", "+sl.pairnum()+", "+id+"");
// if(id%500==10){assert(false);}
if(sl.primary() && (!parsecustom || seen==null || !seen.get(id))){
Read r=sl.toRead(parsecustom);
if(seen!=null){seen.set(id);}
if(parsecustom && r.originalSite==null){
assert(false);
System.err.println("Turned off custom parsing.");
parsecustom=false;
}
//System.out.println(r);
calcStatistics1(r, sl);
}else{
secondary++;
}
}
}
if(tswLoose!=null){tswLoose.poisonAndWait();}
if(tswStrict!=null){tswStrict.poisonAndWait();}
if(reads<-1){reads=primary;}
double tmult=100d/reads;
double mappedB=mapped*tmult;
double retainedB=mappedRetained*tmult;
double truePositiveStrictB=truePositiveStrict*tmult;
double falsePositiveStrictB=falsePositiveStrict*tmult;
double truePositiveLooseB=truePositiveLoose*tmult;
double falsePositiveLooseB=falsePositiveLoose*tmult;
double falseNegativeB=(reads-mapped)*tmult;
double discardedB=discarded*tmult;
double ambiguousB=ambiguous*tmult;
System.out.println();
System.out.println("Mapping Statistics for "+args[0]+":");
System.out.println("primary alignments: \t"+primary+" found of "+reads+" expected");
System.out.println("secondary alignments: \t"+secondary+" found");
System.out.println(String.format(Locale.ROOT, "mapped: \t"+(mappedB<10?" ":"")+"%.3f", mappedB)+"%");
System.out.println(String.format(Locale.ROOT, "retained: \t"+(retainedB<10?" ":"")+"%.3f", retainedB)+"%");
System.out.println(String.format(Locale.ROOT, "discarded: \t"+(discardedB<10?" ":"")+"%.3f", discardedB)+"%");
System.out.println(String.format(Locale.ROOT, "ambiguous: \t"+(ambiguousB<10?" ":"")+"%.3f", ambiguousB)+"%");
if(parsecustom){
System.out.println();
System.out.println("Strict correctness (both ends exactly correct):");
System.out.println(String.format(Locale.ROOT, "true positive: \t"+(truePositiveStrictB<10?" ":"")+"%.3f", truePositiveStrictB)+"%");
System.out.println(String.format(Locale.ROOT, "false positive: \t"+(falsePositiveStrictB<10?" ":"")+"%.3f", falsePositiveStrictB)+"%");
System.out.println();
System.out.println("Loose correctness (one end approximately correct):");
System.out.println(String.format(Locale.ROOT, "true positive: \t"+(truePositiveLooseB<10?" ":"")+"%.3f", truePositiveLooseB)+"%");
System.out.println(String.format(Locale.ROOT, "false positive: \t"+(falsePositiveLooseB<10?" ":"")+"%.3f", falsePositiveLooseB)+"%");
}
System.out.println();
System.out.println(String.format(Locale.ROOT, "false negative: \t"+(falseNegativeB<10?" ":"")+"%.3f", falseNegativeB)+"%");
if(printerr){
System.err.println();
System.err.println("Mapping Statistics for "+args[0]+":");
System.err.println("primary alignments: \t"+primary+" found of "+reads+" expected");
System.err.println("secondary alignments: \t"+secondary+" found");
System.err.println(String.format(Locale.ROOT, "mapped: \t"+(mappedB<10?" ":"")+"%.3f", mappedB)+"%");
System.err.println(String.format(Locale.ROOT, "retained: \t"+(retainedB<10?" ":"")+"%.3f", retainedB)+"%");
System.err.println(String.format(Locale.ROOT, "discarded: \t"+(discardedB<10?" ":"")+"%.3f", discardedB)+"%");
System.err.println(String.format(Locale.ROOT, "ambiguous: \t"+(ambiguousB<10?" ":"")+"%.3f", ambiguousB)+"%");
if(parsecustom){
System.err.println();
System.err.println("Strict correctness (both ends exactly correct):");
System.err.println(String.format(Locale.ROOT, "true positive: \t"+(truePositiveStrictB<10?" ":"")+"%.3f", truePositiveStrictB)+"%");
System.err.println(String.format(Locale.ROOT, "false positive: \t"+(falsePositiveStrictB<10?" ":"")+"%.3f", falsePositiveStrictB)+"%");
System.err.println();
System.err.println("Loose correctness (one end approximately correct):");
System.err.println(String.format(Locale.ROOT, "true positive: \t"+(truePositiveLooseB<10?" ":"")+"%.3f", truePositiveLooseB)+"%");
System.err.println(String.format(Locale.ROOT, "false positive: \t"+(falsePositiveLooseB<10?" ":"")+"%.3f", falsePositiveLooseB)+"%");
}
System.err.println();
System.err.println(String.format(Locale.ROOT, "false negative: \t"+(falseNegativeB<10?" ":"")+"%.3f", falseNegativeB)+"%");
}
}
public static void calcStatistics1(final Read r, SamLine sl){
primary++;
if(r.discarded()/* || r.mapScore==0*/){
discarded++;
unmapped++;
}else if(r.ambiguous()){
// assert(r.mapped()) : "\n"+r+"\n"+sl+"\n";
if(r.mapped()){mapped++;}
ambiguous++;
}else if(r.mapScore<1){
unmapped++;
}else if(r.mapScore<=minQuality){
if(r.mapped()){mapped++;}
ambiguous++;
}else{
if(!r.mapped()){
unmapped++;
}else{
mapped++;
mappedRetained++;
if(parsecustom){
Header h=new Header(sl.qname, sl.pairnum());
boolean strict=isCorrectHit(sl, h);
boolean loose=isCorrectHitLoose(sl, h);
// System.err.println(sl.strand()+", "+sl.start(true, true)+", "+sl.stop(sl.start(true, true), true, true)+", "+sl.rnameS());
// System.err.println(h.strand+", "+h.start+", "+h.stop+", "+h.rname);
// System.err.println(strict+", "+loose);
// System.err.println();
// assert(false);
// SiteScore os=r.originalSite;
// System.out.println("A1: "+os);
// assert(os!=null);
// final int trueChrom=os.chrom;
// final byte trueStrand=os.strand;
// final int trueStart=os.start;
// final int trueStop=os.stop;
// // System.err.println();
// // System.err.println(sl);
// // System.err.println();
// // System.err.println(r);
// // System.err.println();
// SiteScore ss=new SiteScore(r.chrom, r.strand(), r.start, r.stop, 0, 0);
// byte[] originalContig=sl.originalContig();
// if(BLASR){
// originalContig=(originalContig==null || Tools.indexOf(originalContig, (byte)'/')<0 ? originalContig :
// KillSwitch.copyOfRange(originalContig, 0, Tools.lastIndexOf(originalContig, (byte)'/')));
// }
// int cstart=sl.originalContigStart();
//
// // System.out.println("A2: "+trueStart+", "+cstart);
// boolean strict=isCorrectHit(ss, trueChrom, trueStrand, trueStart, trueStop, THRESH, originalContig, sl.rname(), cstart, r);
// boolean loose=isCorrectHitLoose(ss, trueChrom, trueStrand, trueStart, trueStop, THRESH+THRESH2, originalContig, sl.rname(), cstart);
// if(!strict){
// System.out.println(ss+", "+new String(originalContig)+", "+new String(sl.rname()));
// assert(false);
// }
// System.out.println("loose = "+loose+" for "+r.toText());
if(loose){
// System.err.println("TPL\t"+trueChrom+", "+trueStrand+", "+trueStart+", "+trueStop+"\tvs\t"
// +ss.chrom+", "+ss.strand+", "+ss.start+", "+ss.stop);
truePositiveLoose++;
}else{
// System.err.println("FPL\t"+trueChrom+", "+trueStrand+", "+trueStart+", "+trueStop+"\tvs\t"
// +ss.chrom+", "+ss.strand+", "+ss.start+", "+ss.stop);
falsePositiveLoose++;
if(tswLoose!=null){
if(ffLoose.samOrBam()){
tswLoose.println(sl.toText());
}else{
tswLoose.println(r);
}
}
}
if(strict){
// System.err.println("TPS\t"+trueStart+", "+trueStop+"\tvs\t"+ss.start+", "+ss.stop);
truePositiveStrict++;
}else{
// System.err.println("FPS\t"+trueStart+", "+trueStop+"\tvs\t"+ss.start+", "+ss.stop);
falsePositiveStrict++;
if(tswStrict!=null){
if(ffStrict.samOrBam()){
tswStrict.println(sl.toText());
}else{
tswStrict.println(r);
}
}
}
}
}
}
}
public static boolean isCorrectHit(SamLine sl, Header h){
if(!sl.mapped()){return false;}
if(h.strand!=sl.strand()){return false;}
int start=sl.start(true, true);
int stop=sl.stop(start, true, true);
if(h.start!=start){return false;}
if(h.stop!=stop){return false;}
if(!h.rname.equals(sl.rnameS())){return false;}
return true;
}
public static boolean isCorrectHitLoose(SamLine sl, Header h){
if(!sl.mapped()){return false;}
if(h.strand!=sl.strand()){return false;}
int start=sl.start(true, true);
int stop=sl.stop(start, true, true);
if(!h.rname.equals(sl.rnameS())){return false;}
if(h.start!=start){return false;}
if(h.stop!=stop){return false;}
return(absdif(h.start, start)<=THRESH2 || absdif(h.stop, stop)<=THRESH2);
}
// public static boolean isCorrectHit(SiteScore ss, int trueChrom, byte trueStrand, int trueStart, int trueStop, int thresh,
// byte[] originalContig, byte[] contig, int cstart, Read r){
//
// final int cstop=cstart+trueStop-trueStart;
//
//// System.out.println("\n"+r.id);
//// System.out.println(" \tstrand"+/*"\tchrom"+*/"\tstart\tstop\t");//+"scaf");
//// System.out.println("Original:\t"+trueStrand+/*"\t"+trueChrom+*/"\t"+trueStart+"\t"+trueStop+"\t");//+new String(originalContig));
//// System.out.println("Mapped: \t"+ss.strand+/*"\t"+ss.chrom+*/"\t"+ss.start+"\t"+ss.stop+"\t");//+new String(contig));
//// System.out.println("cs: \t"+trueStrand+/*"\t"+trueChrom+*/"\t"+cstart+"\t"+cstop+"\t");//+new String(contig));
//
// if(ss.strand!=trueStrand){return false;}
// if(originalContig!=null){
// if(!Arrays.equals(originalContig, contig)){return false;}
// }else{
// if(ss.chrom!=trueChrom){return false;}
// }
//
// assert(ss.stop>ss.start) : ss.toText()+", "+trueStart+", "+trueStop;
// assert(trueStop>trueStart) : ss.toText()+", "+trueStart+", "+trueStop;
//// return (absdif(ss.start, trueStart)<=thresh && absdif(ss.stop, trueStop)<=thresh);
// return (absdif(ss.start, cstart)<=thresh && absdif(ss.stop, cstop)<=thresh);
// }
//
//
// public static boolean isCorrectHitLoose(SiteScore ss, int trueChrom, byte trueStrand, int trueStart, int trueStop, int thresh,
// byte[] originalContig, byte[] contig, int cstart){
// if(ss.strand!=trueStrand){return false;}
// if(originalContig!=null){
// if(!Arrays.equals(originalContig, contig)){return false;}
// }else{
// if(ss.chrom!=trueChrom){return false;}
// }
//
// assert(ss.stop>ss.start) : ss.toText()+", "+trueStart+", "+trueStop;
// assert(trueStop>trueStart) : ss.toText()+", "+trueStart+", "+trueStop;
// int cstop=cstart+trueStop-trueStart;
//// return (absdif(ss.start, trueStart)<=thresh || absdif(ss.stop, trueStop)<=thresh);
// return (absdif(ss.start, cstart)<=thresh || absdif(ss.stop, cstop)<=thresh);
// }
private static final int absdif(int a, int b){
return a>b ? a-b : b-a;
}
public static FileFormat ffLoose=null;
public static FileFormat ffStrict=null;
public static TextStreamWriter tswLoose=null;
public static TextStreamWriter tswStrict=null;
public static int truePositiveStrict=0;
public static int falsePositiveStrict=0;
public static int truePositiveLoose=0;
public static int falsePositiveLoose=0;
public static int mapped=0;
public static int mappedRetained=0;
public static int unmapped=0;
public static int discarded=0;
public static int ambiguous=0;
public static long lines=0;
public static long primary=0;
public static long secondary=0;
public static int minQuality=3;
public static boolean parsecustom=true;
public static boolean printerr=false;
public static int THRESH2=20;
public static boolean BLASR=false;
public static boolean USE_BITSET=true;
public static BitSet seen=null;
}
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