Merge pull request #132 from ryan-williams/fastq

Fix a bug in bamToFastq and add a test for it

.gitignore

@@ -7,3 +7,4 @@ docs/_build/
 src/utils/version/version_git.h
 .project
 .cproject
+nbproject

src/bamToFastq/bamToFastq.cpp

@@ -79,20 +79,26 @@ void BamToFastq::PairedFastq() {
     reader.Open(_bamFile);
     // rip through the BAM file and convert each mapped entry to BEDPE
     BamAlignment bam1, bam2;
-    while (reader.GetNextAlignment(bam1)) {
+    bool shouldConsumeReads = true;
+    while (true) {
         
-        reader.GetNextAlignment(bam2);        
+        if (shouldConsumeReads) {
+            if (!reader.GetNextAlignment(bam1) || !reader.GetNextAlignment(bam2)) break;
+        } else {
+            shouldConsumeReads = true;
+        }
         if (bam1.Name != bam2.Name) {
             while (bam1.Name != bam2.Name)
             {
                 if (bam1.IsPaired()) 
                 {
                     cerr << "*****WARNING: Query " << bam1.Name
-                         << " is marked as paired, but it's mate does not occur"
+                         << " is marked as paired, but its mate does not occur"
                          << " next to it in your BAM file.  Skipping. " << endl;
                 }
                 bam1 = bam2;
-                reader.GetNextAlignment(bam2);
+                if (!reader.GetNextAlignment(bam2)) break;
+                shouldConsumeReads = false;
             }
         }
         else if (bam1.IsPaired() && bam2.IsPaired()) {

test/bamtofastq/golden.fq

+@paired-1/1
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+DDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
+@paired-2/1
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

test/bamtofastq/golden.fq2

+@paired-1/2
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
++
+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
+@paired-2/2
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++
+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH

test/bamtofastq/test-bamtofastq.sh

+BT=${BT-../../bin/bedtools}
+
+check()
+{
+	if diff $1 $2; then
+    	echo ok
+	else
+    	echo fail
+	fi
+}
+
+samtools view -Sb test.sam > test.bam 2> /dev/null
+
+$BT bamtofastq -i test.bam -fq test.fq -fq2 test.fq2 2> /dev/null
+
+check test.fq golden.fq
+check test.fq2 golden.fq2
+
+rm test.bam test.fq test.fq2
+

test/bamtofastq/test.sam

+@HD	VN:1.0	GO:none	SO:coordinate
+@SQ	SN:chr1	LN:249250621
+paired-1	1	chr1	1	40	30M	*	0	0	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	DDDDDDDDDDDDDDDDDDDDDDDDDDDDDD	MD:Z:50
+paired-1	1	chr1	1	100	30M	*	0	0	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	MD:Z:50
+unpaired	1	chr1	1	100	30M	*	0	0	GAAGGCCACCGCCGCGGTTATTTTCCTTCA	CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI	MD:Z:50
+paired-2	1	chr1	1	40	30M	*	0	0	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	MD:Z:50
+paired-2	1	chr1	1	100	30M	*	0	0	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH	MD:Z:50