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New: added Barcode qualities keeping in FastqToBam #932

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New: added Barcode qualities keeping in FastqToBam #932

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3 changes: 3 additions & 0 deletions src/main/scala/com/fulcrumgenomics/fastq/FastqToBam.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -92,6 +92,7 @@ class FastqToBam
@arg(flag='s', doc="If true, queryname sort the BAM file, otherwise preserve input order.") val sort: Boolean = false,
@arg(flag='u', doc="Tag in which to store molecular barcodes/UMIs.") val umiTag: String = ConsensusTags.UmiBases,
@arg(flag='q', doc="Tag in which to store molecular barcode/UMI qualities.") val umiQualTag: Option[String] = None,
@arg(flag='b', doc="Tag in which to store sample barcode qualities.") val smpQualTag: Option[String] = None,
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since we have a short flag, it's not the worst to have a fully qualified long name

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@arg(flag='b', doc="Tag in which to store sample barcode qualities.") val smpQualTag: Option[String] = None,
@arg(flag='b', doc="Tag in which to store sample barcode qualities.") val sampleBarcodeQualTag: Option[String] = None,

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What do you thin about just making this a boolean value, and then hard code QT below (like we do for BC) since thats the recommended tag from the SAM spec?

@arg(flag='n', doc="Extract UMI(s) from read names and prepend to UMIs from reads.") val extractUmisFromReadNames: Boolean = false,
@arg( doc="Read group ID to use in the file header.") val readGroupId: String = "A",
@arg( doc="The name of the sequenced sample.") val sample: String,
Expand Down Expand Up @@ -157,6 +158,7 @@ class FastqToBam
try {
val subs = fqs.iterator.zip(structures.iterator).flatMap { case(fq, rs) => rs.extract(fq.bases, fq.quals) }.toIndexedSeq
val sampleBarcode = subs.iterator.filter(_.kind == SampleBarcode).map(_.bases).mkString("-")
val smpQual = subs.iterator.filter(_.kind == SampleBarcode).map(_.quals).mkString(" ")
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  1. updated the name as per above
  2. Assuming you'll use QT as per the SAM spec, in which case we want it hyphen delimited:

The recommended implementation concatenates all the barcodes and places a hyphen (‘-’) between the barcodes from the same template.

Suggested change
val smpQual = subs.iterator.filter(_.kind == SampleBarcode).map(_.quals).mkString(" ")
val sampleBarcodeQualTag = subs.iterator.filter(_.kind == SampleBarcode).map(_.quals).mkString("-")

val umi = subs.iterator.filter(_.kind == MolecularBarcode).map(_.bases).mkString("-")
val umiQual = subs.iterator.filter(_.kind == MolecularBarcode).map(_.quals).mkString(" ")
val templates = subs.iterator.filter(_.kind == Template).toList
Expand All @@ -181,6 +183,7 @@ class FastqToBam
}

if (sampleBarcode.nonEmpty) rec("BC") = sampleBarcode
if (smpQual.nonEmpty) smpQualTag.foreach(rec(_) = smpQual)
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I'd hard code to QT as per above


// Set the UMI on the read depending on whether we got UMIs from the read names, reads or both
(umi, umiFromReadName) match {
Expand Down