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fix: mapped header records should overwrite unmapped in ZipperBams #963

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merged 1 commit into from
Jan 31, 2024
Merged

fix: mapped header records should overwrite unmapped in ZipperBams #963

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14 changes: 9 additions & 5 deletions src/main/scala/com/fulcrumgenomics/bam/ZipperBams.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -87,11 +87,15 @@ private[bam] object ZipperBams extends LazyLogging {
val header = new SAMFileHeader(dict)

// Copy over comments, RGs and PGs, letting mapped override unmapped if there are conflicts
Iterator(unmapped, mapped).foreach { old =>
old.getComments.iterator().foreach(header.addComment)
old.getReadGroups.iterator().foreach(header.addReadGroup)
old.getProgramRecords.iterator().foreach(header.addProgramRecord)
}
val mappedComments = mapped.getComments.toSet
val mappedReadGroups = mapped.getReadGroups.toSet
val mappedProgramRecords = mapped.getProgramRecords.toSet
unmapped.getComments.filterNot(mappedComments.contains).foreach(header.addComment)
unmapped.getReadGroups.filterNot(mappedReadGroups.contains).foreach(header.addReadGroup)
unmapped.getProgramRecords.filterNot(mappedProgramRecords.contains).foreach(header.addProgramRecord)
mapped.getComments.foreach(header.addComment)
mapped.getReadGroups.foreach(header.addReadGroup)
mapped.getProgramRecords.foreach(header.addProgramRecord)

// Set the sort and group order
header.setSortOrder(unmapped.getSortOrder)
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