Add TemplateCoordinate sort order to the usage of SortBam (#993)

* Add TemplateCoordinate sort order to the usage of SortBam
fulcrumgenomics · May 30, 2024 · 8d31cf3 · 8d31cf3
1 parent d5b38ca
commit 8d31cf3
Showing 1 changed file with 4 additions and 0 deletions.
diff --git 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