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Add TemplateCoordinate sort order to the usage of SortBam (#993)
* Add TemplateCoordinate sort order to the usage of SortBam
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src/main/scala/com/fulcrumgenomics/bam/SortBam.scala

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@@ -41,6 +41,10 @@ import com.fulcrumgenomics.util.Io
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|and several
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|4. **RandomQuery**: sorts the reads into a random order but keeps reads with the same
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| queryname together. The ordering is deterministic for any given input.
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|5. **TemplateCoordinate**: 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
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| read pair, library, the molecular identifier (MI tag), read name, and if R1 has the lower
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| coordinates of the pair.
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|
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|Uses a temporary directory to buffer sets of sorted reads to disk. The number of reads kept in memory
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|affects memory use and can be changed with the `--max-records-in-ram` option. The temporary directory

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