bamchecksort1
Check sort order of a bam file
Usage
bamchecksort [options]
Overview
bamchecksort reads a BAM file via standard input and checks the sort order of the records in the file. For query name sorted files the program strictly checks the order used by the bamsort program, i.e. it requires reads marked as read 1 to appear before such marked as read 2 for lines with equal names.
The following key=value pairs can be given:
verbose=<1>: Valid values are
1:
|
print progress report on standard error |
|---|---|
0:
|
do not print progress report |
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).