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Add TemplateCoordinate sort order to the usage of SortBam #993

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May 30, 2024
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Add TemplateCoordinate sort order to the usage of SortBam #993

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Add TemplateCoordinate sort order to the usage of SortBam
nh13 May 30, 2024
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Update src/main/scala/com/fulcrumgenomics/bam/SortBam.scala
nh13 May 30, 2024
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4 changes: 4 additions & 0 deletions src/main/scala/com/fulcrumgenomics/bam/SortBam.scala
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Expand Up @@ -41,6 +41,10 @@ import com.fulcrumgenomics.util.Io
|and several
|4. **RandomQuery**: sorts the reads into a random order but keeps reads with the same
| queryname together. The ordering is deterministic for any given input.
|5. **TemplateCoordinate**: sorts the reads The sort order used by `GroupReadByUmi`. Sorts reads by
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| the earlier unclipped 5' coordinate of the read pair, the higher unclipped 5' coordinate of the
| read pair, library, the molecular identifier (MI tag), read name, and if R1 has the lower
| coordinates of the pair.
|
|Uses a temporary directory to buffer sets of sorted reads to disk. The number of reads kept in memory
|affects memory use and can be changed with the `--max-records-in-ram` option. The temporary directory
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