feat: add an option to store sample base qualities in the QT for FastqToBam #933
Conversation
| @@ -322,6 +322,24 @@ class FastqToBamTest extends UnitSpec { | |||
| recs(3).basesString shouldBe "CCCCCCCCCC" | |||
| } | |||
|
|
|||
| it should "extract sample barcode qualities when requested" in { | |||
There was a problem hiding this comment.
@galaxy001, take a look at the inputs and outputs and see if this suffices.
Codecov ReportPatch coverage:
❗ Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the GitHub App Integration for your organization. Read more. Additional details and impacted files@@ Coverage Diff @@
## main #933 +/- ##
=======================================
Coverage 95.60% 95.60%
=======================================
Files 126 126
Lines 7305 7307 +2
Branches 517 507 -10
=======================================
+ Hits 6984 6986 +2
Misses 321 321
Flags with carried forward coverage won't be shown. Click here to find out more.
☔ View full report in Codecov by Sentry. |
| @@ -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(doc="Store the sample barcode qualities in the QT Tag.") val storeSampleBarcodeQualities: Boolean = false, | |||
There was a problem hiding this comment.
Why there is no flag ? What will the option char for enabling QT ?
There was a problem hiding this comment.
Use the full command line option --store-sample-barcode-qualities. I don't think there's a flag that makes sense, and likely since folks are implementing this in a workflow software, I don't think it's too onerous. If you really want one, I'd pick x since it's sufficiently different than the others.
There was a problem hiding this comment.
I'd probably just add -Q if it were up to me
| @@ -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(doc="Store the sample barcode qualities in the QT Tag.") val storeSampleBarcodeQualities: Boolean = false, | |||
There was a problem hiding this comment.
I'd probably just add -Q if it were up to me
| recs(2).apply[String]("BC") shouldBe "GAA-TCG" | ||
| recs(2).apply[String]("QT") shouldBe "CDE IJK" | ||
| } | ||
|
|
There was a problem hiding this comment.
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?
Alternative to #932 to implement #931