v1.0.15

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

v1.0.14

BamUtil Version 1.0.14 - Released 7/8/2015

v1.0.13

BamUtil Version 1.0.13 - Released 2/20/2015

• https://github.com/statgen/bamUtil/archive/v1.0.13.tar.gz
• Requires, but does not include: libStatGen version 1.0.13
• Makefule Updates
  • Improve logic to determine actual path for the library
  • Update to append to USER_COMPILE_VARS even if specified on the command line
• Update writeRegion
  • Add option to specify readnames to keep in a file
  • Fixed bug that if a read overlapped 2 BED positions, it was printed twice
• Update to bam2FastQ
  • Update to skip non-primary reads
• Update to polishBam
  • Update to handle '\t' string inputs and to add CO option
  • Fix MD5sum calculation to convert fasta to uppercase prior to calculating

v1.0.12

BamUtil.1.0.12 Release Notes - Released 5/14/2014

Requires libStatGen version 1.0.12 : https://github.com/statgen/libStatGen

• Update mergeBam
  • Add a regions option
• Update to squeeze, revert, diff
  • Also accept ',' instead of just ';' as the delimiter in the input tags string.

v1.0.11

BamUtil.1.0.11 Release Notes - Released 2/28/2014

• Requires libStatGen version 1.0.11 : https://github.com/statgen/libStatGen
• Update 'splitBam' & 'polishBam'
  • Update to work properly if log & output file are not specified (no longer creates '.log')
• Update Main dummy/example tool to indicate the correct tool
• Update to 'bam2FastQ', 'clipOverlap', 'filter', 'mergeBam', 'splitBam', 'squeeze', 'stats'
  • Cleanup usage/parameter descriptions
• Update 'revert'
  • Update compatibility with libStatGen due to 'B' & 'f' tag handling updates
• Add tests for 'B' & 'f' tags