Clarification in parametersDefault.
@@ -319,7 +319,7 @@ outSAMfilter None
outSAMmultNmax -1
- int: max number of multiple alignments for a read that will be output to the SAM/BAM files.
+ int: max number of multiple alignments for a read that will be output to the SAM/BAM files. Note that if this value is not equal to -1, the top scoring alignment will be output first
-1 ... all alignments (up to --outFilterMultimapNmax) will be output
outSAMtlen 1
