Package: picard-tools / 2.8.1+dfsg-1

30-tests-fix-dataprovider.patch Patch series | download
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Description: fix data provider requirements
Author: Sascha Steinbiss <satta@debian.org>
--- a/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
+++ b/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
@@ -21,22 +21,22 @@
 
     @DataProvider(name = "collectHsMetricsDataProvider")
     public Object[][] targetedIntervalDataProvider() {
-        final String referenceFile = TEST_DIR + "/chrM.fasta";
-        final String intervals = TEST_DIR + "/chrM.interval_list";
-        final String twoSmallIntervals = TEST_DIR + "/two-small.interval_list";
+        final String referenceFile = TEST_DIR.getAbsolutePath() + "/chrM.fasta";
+        final String intervals = TEST_DIR.getAbsolutePath() + "/chrM.interval_list";
+        final String twoSmallIntervals = TEST_DIR.getAbsolutePath() + "/two-small.interval_list";
 
         return new Object[][] {
                 // two reads, each has 100 bases. bases in one read are medium quality (20), in the other read poor quality (10).
                 // test that we exclude half of the bases
-                {TEST_DIR + "/lowbaseq.sam",    intervals, 1, 10, true,  2, 200, 0.5, 0.0, 0.50, 0.0,   1000},
+                {TEST_DIR.getAbsolutePath() + "/lowbaseq.sam",    intervals, 1, 10, true,  2, 200, 0.5, 0.0, 0.50, 0.0,   1000},
                 // test that read 2 (with mapping quality 1) is filtered out with minimum mapping quality 2
-                {TEST_DIR + "/lowmapq.sam",     intervals, 2, 0, true,  2, 202, 0,   0.0, 0.505, 0.0,   1000},
+                {TEST_DIR.getAbsolutePath() + "/lowmapq.sam",     intervals, 2, 0, true,  2, 202, 0.0, 0.0, 0.505, 0.0,   1000},
                 // test that we clip overlapping bases
-                {TEST_DIR + "/overlapping.sam", intervals, 0, 0, true,  2, 202, 0,   0.5, 0.505, 0.505, 1000},
+                {TEST_DIR.getAbsolutePath() + "/overlapping.sam", intervals, 0, 0, true,  2, 202, 0.0, 0.5, 0.505, 0.505, 1000},
                 // test that we do not clip overlapping bases
-                {TEST_DIR + "/overlapping.sam", intervals, 0, 0, false, 2, 202, 0,   0.0, 0.505, 0.505, 1000},
+                {TEST_DIR.getAbsolutePath() + "/overlapping.sam", intervals, 0, 0, false, 2, 202, 0.0, 0.0, 0.505, 0.505, 1000},
                 // A read 10 base pairs long. two intervals: one maps identically to the read, other does not overlap at all
-                {TEST_DIR + "/single-short-read.sam", twoSmallIntervals, 20, 20, true, 1, 10, 0.0, 0.0, 0.5, 0.0, 1000 }
+                {TEST_DIR.getAbsolutePath() + "/single-short-read.sam", twoSmallIntervals, 20, 20, true, 1, 10, 0.0, 0.0, 0.5, 0.0, 1000 }
 
         };
     }