fast gapped read alignment with bowtie 2

Fixed an issue that would sometimes cause deadlocks in bowtie2 when running multithreaded.

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

This issue would result in the wrong index type being chosen and only happened with GZip compressed files.

Fixed an issue causing bowtie2-build to sometimes incorrectly calculate input size.

This change seeks to address the assumption that bowtie2-build ran successfully without building the reverse indexes. The extension is removed only upon successful build. tmp extension to index files currenlty being built. This issue would subsequently result in sequence data, being left out from alignment SAM header.

Fixed an issue causing masked-sequence metadata to be omitted from index.

Implemented thread pool to address performance regressions introduced during the switch to C++11 threads.

Appended GO:query to SAM entry to indicate that reads are grouped by query name, bump SAM version to 1.5 to indicate support for this change.

Fixed an issue causing bowtie2 to produce mangled SAM output when specifying -sam-append-comment together with the -passthrough option.Fixed an issue causing bowtie2 to drop certain optional fields when when aligning BAM reads with the -preserve-tags option.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.See the Index zone page for details on the best ways to obtain this data, including from the AWS cloud. Index storage is thanks to AWS Public Datasets program.

bt2 format and are compatible with both Bowtie 2 and with Bowtie as of v1.2.3

Fast gapped read alignment with bowtie 2