Revisions of bowtie2
Dominique Leuenberger (dimstar_suse)
accepted
request 746523
from
Atri Bhattacharya (badshah400)
(revision 6)
initialized devel package after accepting 746523
Pierre Bonamy (flyos)
accepted
request 752540
from
Atri Bhattacharya (badshah400)
(revision 5)
- Use %%license to install LICENSE file.
Pierre Bonamy (flyos)
accepted
request 746398
from
Atri Bhattacharya (badshah400)
(revision 4)
- 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
Pierre Bonamy (flyos)
accepted
request 580966
from
Atri Bhattacharya (badshah400)
(revision 3)
- 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.
Pierre Bonamy (flyos)
accepted
request 520633
from
Martin Pluskal (pluskalm)
(revision 2)
- Update to version 2.3.2:
Matthias Mailänder (Mailaender)
accepted
request 397077
from
Pierre Bonamy (flyos)
(revision 1)
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.
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