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Misc cleanup needed for bigdatagenomics/cannoli#65 #1704

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merged 2 commits into from
Sep 12, 2017
Merged

Misc cleanup needed for bigdatagenomics/cannoli#65 #1704

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2a1e13a
[ADAM-1702] Validate read numbers in InterleavedFASTQInFormatter.
fnothaft Aug 30, 2017
f386347
[ADAM-1703] Expose ValidationStringency in AnySAMOutFormatter.
fnothaft Aug 30, 2017
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14 changes: 12 additions & 2 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.scala
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Expand Up @@ -80,8 +80,18 @@ class InterleavedFASTQInFormatter private (
outputOriginalBaseQualities = writeOriginalQualities) + "\n"

// write both to the output stream
os.write(fastq1.getBytes)
os.write(fastq2.getBytes)
// ensure that reads are ordered properly if ordering is known (see #1702)
if (read1.getReadInFragment == 0 &&
read2.getReadInFragment == 1) {
os.write(fastq1.getBytes)
os.write(fastq2.getBytes)
} else if (read1.getReadInFragment == 1 &&
read2.getReadInFragment == 0) {
os.write(fastq2.getBytes)
os.write(fastq1.getBytes)
} else {
log.warn("Improper pair of reads in fragment %s. Dropping...".format(p))
}
})
}
}
5 changes: 4 additions & 1 deletion adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.scala
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Expand Up @@ -29,7 +29,9 @@ import scala.collection.mutable.ListBuffer
* An OutFormatter that automatically infers whether the piped input is SAM or
* BAM. Autodetecting streamed CRAM is not currently supported.
*/
class AnySAMOutFormatter extends OutFormatter[AlignmentRecord] {
case class AnySAMOutFormatter(stringency: ValidationStringency) extends OutFormatter[AlignmentRecord] {

def this() = this(ValidationStringency.STRICT)

/**
* Reads alignment records from an input stream. Autodetects SAM/BAM format.
Expand All @@ -41,6 +43,7 @@ class AnySAMOutFormatter extends OutFormatter[AlignmentRecord] {

// make reader
val reader = SamReaderFactory.makeDefault()
.validationStringency(stringency)
.open(SamInputResource.of(is))

SAMIteratorConverter(reader)
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