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v2.4.0-beta2

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@ch4rr0 ch4rr0 released this 06 Feb 15:02
· 401 commits to bug_fixes since this release

New changes:

  • Fixed an issue in BAM pattern source where one thread would prematurely close the read file pointer
    resulting in other threads crashing because of "Bad file descriptor" errors.

Changes from first beta

  • Fixed an issue that would causes bowtie2 to crash with --no-1mm-upfront specified
  • Modified bowtie2-build script to better handle of flags and positional parameters
  • Migrated all python scripts to python3
  • Added support for wildcards input files tobowtie2 wrapper script e.g.
    bowtie2 -x index -q *.fq as opposed to bowtie2 -x index -q 1.fq,2.fq,3.fq...
  • Fixed an issue causing bowtie2 to incorrectly process read names see #265
  • Added support for allowing presets to be overridden by more specific options e.g
    bowtie2 -x index --local --very-fast-local --L22 -q reads.fq will cause bowtie2 to use a seed length
    or 22 instead of a seed length of 25 that's configured for --very-fast-local preset.
  • Modified SAM output for -k/-a so that supplementary alignments get assigned a MAPQ of 255
  • Fixed an issue that somtimes causes bowtie2-build to not generate reverse index files
  • Added preliminary support for ppc64le architectures with the help of SIMDE project see #271 for details.