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docs: specify order of clipping operations in ClipBam docs #1143

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clintval merged 3 commits into from
Mar 4, 2026
Merged

docs: specify order of clipping operations in ClipBam docs #1143

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docs: specify order of clipping operations in ClipBam docs
clintval Mar 4, 2026
fb9d822
Update src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala
clintval Mar 4, 2026
ed4f04c
Update src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala
clintval Mar 4, 2026
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7 changes: 7 additions & 0 deletions src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala
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Expand Up @@ -68,6 +68,13 @@ import htsjdk.samtools.SamPairUtil
|The `--upgrade-clipping` parameter will convert all existing clipping in the input to the given more stringent mode:
|from `Soft` to either `SoftWithMask` or `Hard`, and `SoftWithMask` to `Hard`. In all other cases, clipping remains
|the same prior to applying any other clipping criteria.
|
|The order of operations for clipping is:
|
|1. Upgrade of clipping if `--upgrade-clipping` is specified
|2. Any fixed 5-prime or 3-prime clippings for R1 and/or R2
|3. Clipping of overlapping bases in paired reads if `--clip-overlapping-reads` is specified
|4. Clipping of bases extending past mates in `FR` pairs if `--clip-bases-past-mate` is specified
""")
class ClipBam
( @arg(flag='i', doc="Input SAM or BAM file of aligned reads in coordinate order.") val input: PathToBam,
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