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feat: add an option to store sample base qualities in the QT for FastqToBam #933

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Sep 1, 2023
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feat: add an option to store sample base qualities in the QT for FastqToBam #933

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feat: add an option to store sample base qualities in the QT for Fast…
nh13 Aug 31, 2023
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nh13 Aug 31, 2023
172e0df
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nh13 Sep 1, 2023
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5 changes: 4 additions & 1 deletion 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='Q', doc="Store the sample barcode qualities in the QT Tag.") val storeSampleBarcodeQualities: Boolean = false,
@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 sampleQuals = 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 @@ -166,7 +168,7 @@ class FastqToBam

templates.zipWithIndex.map { case (read, index) =>
// If the template read had no bases, we'll substitute in a single N @ Q2 below to keep htsjdk happy
val empty = read.bases.length == 0
val empty = read.bases.isEmpty

val rec = SamRecord(header)
rec(ReservedTagConstants.READ_GROUP_ID) = this.readGroupId
Expand All @@ -181,6 +183,7 @@ class FastqToBam
}

if (sampleBarcode.nonEmpty) rec("BC") = sampleBarcode
if (storeSampleBarcodeQualities && sampleQuals.nonEmpty) rec("QT") = sampleQuals

// Set the UMI on the read depending on whether we got UMIs from the read names, reads or both
(umi, umiFromReadName) match {
Expand Down
28 changes: 28 additions & 0 deletions src/test/scala/com/fulcrumgenomics/fastq/FastqToBamTest.scala
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Expand Up @@ -322,6 +322,34 @@ class FastqToBamTest extends UnitSpec {
recs(3).basesString shouldBe "CCCCCCCCCC"
}

it should "extract sample barcode qualities when requested" in {
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@galaxy001, take a look at the inputs and outputs and see if this suffices.

val r1 = fq(
FastqRecord("q1:2:3:4:5:6:7", "AAACCCAAAA", "ABCDEFGHIJ"),
FastqRecord("q2:2:3:4:5:6:7", "TAANNNAAAA", "BCDEFGHIJK"),
FastqRecord("q3:2:3:4:5:6:7", "GAACCCTCGA", "CDEFGHIJKL"),
)
val bam = makeTempFile("fastqToBamTest.", ".bam")

Seq(true, false).foreach { storeSampleBarcodeQualities =>
new FastqToBam(input = Seq(r1), output = bam, sample = "s", library = "l", readStructures = Seq(rs("3B3M3B+T")), storeSampleBarcodeQualities = storeSampleBarcodeQualities).execute()
val recs = readBamRecs(bam)
recs should have size 3
recs(0).apply[String]("BC") shouldBe "AAA-AAA"
recs(1).apply[String]("BC") shouldBe "TAA-AAA"
recs(2).apply[String]("BC") shouldBe "GAA-TCG"

if (storeSampleBarcodeQualities) {
recs(0).apply[String]("QT") shouldBe "ABC GHI"
recs(1).apply[String]("QT") shouldBe "BCD HIJ"
recs(2).apply[String]("QT") shouldBe "CDE IJK"
} else {
Range.inclusive(0, 2).foreach { index =>
recs(index).contains("QT") shouldBe false
}
}
}
}

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Could you either add a second pass here, or assert in one of the other tests, that if you don't supply a value for storeSampleBarcodeQualities that the QT tag doesn't get set with anything?

it should "extract UMIs from read names when requested" in {
val r1 = fq(
FastqRecord("q1:2:3:4:5:6:7:ACGT", "AAAAAAAAAA", "=========="),
Expand Down