Picard/fgbio/htsjdk aligned files (such as to a wildtype genome) are of a different sort order to the often-used samtools approach of using samtools fastq and aligning with bwa. Thus this exception is hit when trying to neodisambiguate:
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require( |
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templates.map(_.name).distinct.length <= 1, |
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"Templates with different names found! This can only occur if your SAM sources are queryname sorted using" |
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+ " different implementations, such as with Picard tools versus Samtools. If you have encountered this" |
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+ " exception, then please alert the maintainer!" |
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) |
It might be nice to have a fallback mode that re-sorts the SAM streams if they:
- Say they are queryname sorted
- And appear out of order (parsimony is different sort implementations)
Picard/fgbio/htsjdk aligned files (such as to a wildtype genome) are of a different sort order to the often-used samtools approach of using
samtools fastqand aligning with bwa. Thus this exception is hit when trying to neodisambiguate:neodisambiguate/neodisambiguate/src/io/cvbio/neodisambiguate/bam/Bams.scala
Lines 68 to 73 in db7a512
It might be nice to have a fallback mode that re-sorts the SAM streams if they: