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Fix Adam2fastq in case of read with both reverse and unmapped flags #982

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Fix Adam2fastq in case of read with both reverse and unmapped flags #982

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189a803
Fix Adam2fastq in case read with both reverse and unmapped flags
jpdna Mar 26, 2016
f1b1183
Added test to include fastq generation of unampped reads both with an…
jpdna Mar 29, 2016
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4 changes: 2 additions & 2 deletions adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -75,11 +75,11 @@ class AlignmentRecordConverter extends Serializable {
"@%s%s\n%s\n+\n%s".format(
adamRecord.getReadName,
readNameSuffix,
if (adamRecord.getReadMapped && adamRecord.getReadNegativeStrand)
if (adamRecord.getReadNegativeStrand)
Alphabet.dna.reverseComplement(adamRecord.getSequence)
else
adamRecord.getSequence,
if (adamRecord.getReadMapped && adamRecord.getReadNegativeStrand)
if (adamRecord.getReadNegativeStrand)
qualityScores.reverse
else
qualityScores
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2 changes: 1 addition & 1 deletion adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ class FastqRecordConverter extends Serializable with Logging {
else if (setSecondOfPair) 1
else null
)
.setReadNegativeStrand(null)
.setReadNegativeStrand(false)
.setMateNegativeStrand(null)
.setPrimaryAlignment(null)
.setSecondaryAlignment(null)
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49 changes: 30 additions & 19 deletions adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -219,16 +219,16 @@ class AlignmentRecordConverterSuite extends FunSuite {
assert(secondRecordFastq(1) === "AATTCAAAACCAGCCTGGCCAATATGGTGAAACCTCATCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGTGCGTGCGTGTAGTCCCAGCTACTT")
assert(secondRecordFastq(2) === "+")
assert(secondRecordFastq(3) === "?-DDBEEB=EEEDDEDEEEA:D?5?E?CEBE5ED?D:AEDEDEDED-B,BC0AC,BB6@CDBDEC?BCBAA@5,=8CA-?A>?2:&048<BB5BE#####")

}

test("converting to fastq with unmapped reads") {
//SRR062634.10448889 117 22 16079761 0 * = 16079761 0
// TTTCTTTCTTTTATATATATATACACACACACACACACACACACACATATATGTATATATACACGTATATGTATGTATATATGTATATATACACGTATAT
// @DF>C;FDC=EGEGGEFDGEFDD?DFDEEGFGFGGGDGGGGGGGEGGGGFGGGFGGGGGGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
// RG:Z:SRR062634
test("converting to fastq with unmapped reads where read reverse complemented flag (Ox10) was NOT set") {

// SRR062634.20911784 133 22 16060584 0 35M65S = 16060584 0
// TGTAGTGGCAGGGGCCCGTTATCCCAAACTACCTGGGGGGGGGGGGGGGGGGGAACACCTAAAACCCGGGGGGGGGGGGGTTGGTGGGGGCTTTATCGCA
// GGGGGGGDGG@#########################################################################################
// RG:Z:SRR062634 XC:i:35

val (secondRecord, firstRecord) = getSAMRecordFromReadName("SRR062634.10448889")
val (firstRecord, secondRecord) = getSAMRecordFromReadName("SRR062634.20911784")

assert(firstRecord.getReadInFragment === 1)
assert(secondRecord.getReadInFragment === 0)
Expand All @@ -237,23 +237,34 @@ class AlignmentRecordConverterSuite extends FunSuite {
.toString
.split('\n')

assert(firstRecord.getReadMapped)
assert(firstRecord.getReadNegativeStrand)
assert(firstRecordFastq(0) === "@SRR062634.10448889/2")
assert(firstRecordFastq(1) === "ACCTGTCTCAGCCTCCCAAAGTGCTGCGATTACAGTCATGAGCCACCGCACTTGGCTGGGTTTTCGTTTTCTTTCTTTTATATATATATACACACACACA")
assert(firstRecordFastq(0) === "@SRR062634.20911784/2")
assert(firstRecordFastq(1) === "TGTAGTGGCAGGGGCCCGTTATCCCAAACTACCTGGGGGGGGGGGGGGGGGGGAACACCTAAAACCCGGGGGGGGGGGGGTTGGTGGGGGCTTTATCGCA")
assert(firstRecordFastq(2) === "+")
assert(firstRecordFastq(3) === "GGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGFGEGEEDGGFDF?AEEEBDADEEDEEE;DFC@'B:B=B=B=BADCBCBCA=DA")
assert(firstRecordFastq(3) === "GGGGGGGDGG@#########################################################################################")
}

val secondRecordFastq = adamRecordConverter.convertToFastq(secondRecord, maybeAddSuffix = true)
test("converting to fastq with unmapped reads where reverse complemented flag (0x10) was set") {

//SRR062634.10448889 117 22 16079761 0 * = 16079761 0
// TTTCTTTCTTTTATATATATATACACACACACACACACACACACACATATATGTATATATACACGTATATGTATGTATATATGTATATATACACGTATAT
// @DF>C;FDC=EGEGGEFDGEFDD?DFDEEGFGFGGGDGGGGGGGEGGGGFGGGFGGGGGGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
// RG:Z:SRR062634

val (firstRecord, secondRecord) = getSAMRecordFromReadName("SRR062634.10448889")

assert(firstRecord.getReadInFragment === 0)
assert(secondRecord.getReadInFragment === 1)

val firstRecordFastq = adamRecordConverter.convertToFastq(firstRecord, maybeAddSuffix = true)
.toString
.split('\n')

assert(!secondRecord.getReadMapped)
assert(secondRecord.getReadNegativeStrand)
assert(secondRecordFastq(0) === "@SRR062634.10448889/1")
assert(secondRecordFastq(1) === secondRecord.getSequence)
assert(secondRecordFastq(2) === "+")
assert(secondRecordFastq(3) === secondRecord.getQual)
assert(!firstRecord.getReadMapped)
assert(firstRecord.getReadNegativeStrand)
assert(firstRecordFastq(0) === "@SRR062634.10448889/1")
assert(firstRecordFastq(1) === "ATATACGTGTATATATACATATATACATACATATACGTGTATATATACATATATGTGTGTGTGTGTGTGTGTGTGTGTATATATATATAAAAGAAAGAAA")
assert(firstRecordFastq(2) === "+")
assert(firstRecordFastq(3) === "GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFGGGGGGFGGGFGGGGEGGGGGGGDGGGFGFGEEDFD?DDFEGDFEGGEGE=CDF;C>FD@")
}

test("converting a fragment with no alignments should yield unaligned reads") {
Expand Down