BenLangmead/bowtie2: Version 2.4.5 - Jan 15, 2022

bowtie2

• 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.

• 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.

• Added a new -o/--output option to save the output of bowtie2-inspect to a file instead of being dumped to standard output.