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@ch4rr0 ch4rr0 released this 07 Sep 03:33
· 645 commits to master since this release
v2.3.3
5a979eb

From this release forward prepackaged bowtie2 binaries are now
statically linked to the zlib compression library and, the recommended
threading library, TBB. Users who rely on prepackaged builds are
no longer required to have these packages pre-installed. As a result
of the aforementioned changes legacy packages have been discontinued.

* bowtie2-build now supports gzip-compressed FASTA inputs
* New --xeq parameter for bowtie2 disambiguates the 'M' CIGAR
  flag. When specified, matches are indicated with the '=' operation and
  mismatches with 'X'
* Fixed a possible infinite loop during parallel index building due
  to the compiler optimizing away a loop condition
* Added --soft-clipped-unmapped-tlen parameter for bowtie2 that
  ignores soft-clipped bases when calculating template length (TLEN)
* Added support for multi-line sequences in FASTA read inputs
* Expanded explanation of MD:Z field in manual
* Fixed a crashing bug when output is redirected to a pipe
* Fixed ambiguity in the SEED alignment policy that sometimes caused -N parameter to be ignored
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