BamUtil Version 1.0.15 - Released 03/08/2021
- Update TrimBam to accept -.ubam, etc. Previously it failed if the input/output filename was -.ubam, etc
- Update Dedup and Recab to fail and print an error message when stdin is specified. Both require reading the input file twice. Previously they did not work properly, but produced no error messages.
- ClipOverlap - add option to turn off read name alpha-numeric sort validation
- Mention - for STDOUT in
bam stats --help - Resolves issue of read group info of interleaved output (#38)
- Bam2FastQ update interleave (--merge) to work with splitRG option
- Fixes test files.
- Added custom binning scheme
- Append gz extension to gzipped output.
- Escape percent sign for fprintf.
- Fix case sensitivity bug.
- Replace -T flag with -n to support mac version of ln.
- Add usage command for each tool without outputting error.
- Add error message for no args.
- Change main usage output stream to stdout.
- Add usage & help command to print dialoge and exit.
- Add logic to handle Supplementary reads similar to secondary reads
- Dedup - change message about missing mate from ERROR to WARNING
- Update Makefile.inc to only look for the INCLUDE_MAKE if it is not cloneLib
- Add Validation test to test that cigar and seq length are not validated if seq is '*'
- MateMapByCoord - update to use unordered_map if c++11
- Recab - update to apply maximum quality after binning
- Recab - use logfile name for qemp,etc files if output name is stdout
- Recab - do not write logs with '-' prefix if outputing sam/bam to stdout
- Bam2Fastq update nucleotide to be case insensitive
- Bam2Fastq - add option to limit conversion to fastq to only reads containing a specific position/nulceotide