fix #204

biod · Apr 24, 2016 · 00eb211 · 00eb211
1 parent 6ce358f
commit 00eb211
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Showing 4 changed files with 13 additions and 3 deletions.
diff --git a/.test_suite.sh b/.test_suite.sh
@@ -68,9 +68,17 @@ testIndexUsage() {
 }
 
 testIssue193() {
+    rm -f output_193.txt
     ./build/sambamba depth base test/issue_193.bam > output_193.txt 2>/dev/null
     diff -q output_193.txt test/issue_193_expected_output.txt
     assertEquals 0 $?
 }
 
+testIssue204() {
+    rm -f output_204.txt
+    ./build/sambamba index test/issue_204.bam
+    ./build/sambamba depth region test/issue_204.bam -L 2:166868600-166868813 -T 15 -T 20 -T 25 -m > output_204.txt 2>/dev/null
+    diff -q output_204.txt test/issue_204_expected_output.txt
+}
+
 . shunit2-2.0.3/src/shell/shunit2
diff --git a/sambamba/depth.d b/sambamba/depth.d
@@ -803,10 +803,10 @@ abstract class PerRegionPrinter : ColumnPrinter {
                         if (read.mate_overlap != MateOverlapStatus.past)
                             continue;
                         processCurrentBase(read, id);
+                    } else {
+                        if (read.current_base_quality >= min_base_quality)
+                            cov_per_sample[getSampleId(read)] += 1;
                     }
-
-                    if (read.current_base_quality >= min_base_quality)
-                        cov_per_sample[getSampleId(read)] += 1;
                 }
 
                 foreach (pair; overlapping_mate_positions) {

diff --git a/test/issue_204.bam b/test/issue_204.bam
diff --git a/test/issue_204_expected_output.txt b/test/issue_204_expected_output.txt
@@ -0,0 +1,2 @@
+# chrom	chromStart	chromEnd	readCount	meanCoverage	percentage15	percentage20	percentage25	sampleName
+2	166868599	166868813	29	17.8084	89.7196	29.9065	0	12878
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		# chrom chromStart chromEnd readCount meanCoverage percentage15 percentage20 percentage25 sampleName
		2 166868599 166868813 29 17.8084 89.7196 29.9065 0 12878