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Fixed issues with bowtie2 BAM parser that would cause bowtie2 to
crash when processing input that was encoded with tools other than
samtools e.g. Picard.
Fixed an issue causing bowtie2 to drop certain optional fields when
when aligning BAM reads with the --preserve-tags option.
Fixed an issue causing bowtie2 to produce mangled SAM output when
specifying --sam-append-comment together with the --passthrough
option.
Appended GO:query to SAM @HD entry to indicate that reads are
grouped by query name, bump SAM version to 1.5 to indicate support
for this change.
bowtie2-build
Implemented thread pool to address performance regressions
introduced during the switch to C++11 threads.
Fixed an issue causing masked-sequence metadata to be omitted
from index. This issue would subsequently result in sequence
data, @SQ, being left out from alignment SAM header.
Included .tmp extension to index files currenlty being built.
The extension is removed only upon successful build. This change
seeks to address the assumption that bowtie2-build ran successfully
without building the reverse indexes.
Fixed an issue causing bowtie2-build to sometimes incorrectly
calculate input size. This issue would result in the wrong index type
being chosen and only happened with GZip compressed files.
bowtie2-inspect
Added a new -o/--output option to save the output of bowtie2-inspect to a file instead of being dumped to standard
output.