v2.4.0-beta2
Pre-release
Pre-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 to
bowtie2
wrapper script e.g.
bowtie2 -x index -q *.fq
as opposed tobowtie2 -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
or22
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.