- Update to version 2.5.0:
* Overall improvements in the use of prefetch instructions.
* Made input/output fully asynchronous by using a dedicated
thread.
* Added support for AVX2 256-bit instructions with can be
enabled by setting the SSE_AXV2 environment variable at
compile time.
* Fixed an issue causing bowtie2 to crash when processing ZSTD
files with high compression ratios.
* Changed the way that unique alignments are counted in summary
message to better match up with filters on SAM output.
OBS-URL: https://build.opensuse.org/request/show/1036958
OBS-URL: https://build.opensuse.org/package/show/science/bowtie2?expand=0&rev=19
- Update to version 2.3.5.1:
* Added official support for BAM input files.
* Added official support for CMake build system.
* Added changes to Makefile for creating Reproducible builds
[gh#BenLangmead/bowtie2#210].
* Fix an issue whereby building on aarch64 would require
patching sed commands [gh#BenLangmead/bowtie2#243].
* Fix an issue whereby `bowtie2` would incorrectly throw an
error while processing `--interleaved` input.
- Changes from version 2.3.5:
* Added support for obtaining input reads directly from the
Sequence Read Archive, via NCBI's [NGS language
bindings](https://github.com/ncbi/ngs). This is activated via
the [`--sra-acc`](manual.shtml#bowtie2-options-sra-acc)
option. This implementation is based on Daehwan Kim's in
[HISAT2](https://ccb.jhu.edu/software/hisat2). Supports both
unpaired and paired-end inputs.
* Bowtie 2 now compiles on ARM architectures (via
[gh#BenLangmead/bowtie2#216].
* `--interleaved` can now be combined with FASTA inputs (worked
only with FASTQ before).
* Fixed issue whereby large indexes were not successfully found
in the `$BOWTIE2_INDEXES` directory.
* Fixed input from FIFOs (e.g. via process substitution) to
distinguish gzip-compressed versus uncompressed input.
* Fixed issue whereby arguments containing `bz2` `lz4` were
misinterpretted as files.
* Fixed several compiler warnings.
* Fixed issue whereby both ends of a paired-end read could have
negative TLEN if they exactly coincided
OBS-URL: https://build.opensuse.org/request/show/746398
OBS-URL: https://build.opensuse.org/package/show/science/bowtie2?expand=0&rev=4
- Update to version 2.3.4.1:
* Fixed an issue with --reorder that caused bowtie2 to crash
while reordering SAM output
- Changes from version 2.3.4:
* Fixed major issue causing corrupt SAM output when using many
threads (-p/--threads) on certain systems.
* Fixed an issue whereby bowtie2 processes could overwrite each
others' named pipes on HPC systems.
* Fixed an issue causing bowtie2-build and bowtie2-inspect to
return prematurely on Windows.
* Fixed issues raised by compiler "sanitizers" that could
potentially have caused memory corruption or undefined
behavior.
* Added the "continuous FASTA" input format (-F) for aligning
all the k-mers in the sequences of a FASTA file. Useful for
determining mapability of regions of the genome, and similar
tasks.
- Run sed on binaries to modify env based hashbangs to ones that
directly call executables.
- Drop bowtie2-gcc6.patch; incorporated upstream.
OBS-URL: https://build.opensuse.org/request/show/580966
OBS-URL: https://build.opensuse.org/package/show/science/bowtie2?expand=0&rev=3
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
OBS-URL: https://build.opensuse.org/request/show/397077
OBS-URL: https://build.opensuse.org/package/show/science/bowtie2?expand=0&rev=1
