diff --git a/src/main/scala/com/fulcrumgenomics/bam/SortBam.scala b/src/main/scala/com/fulcrumgenomics/bam/SortBam.scala index 4e9a59360..ad5d63212 100644 --- a/src/main/scala/com/fulcrumgenomics/bam/SortBam.scala +++ b/src/main/scala/com/fulcrumgenomics/bam/SortBam.scala @@ -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**: The sort order used by `GroupReadByUmi`. Sorts reads by + | 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