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chrovis
A DNA Sequence Alignment/Map (SAM) library for Clojure
This PR resolves #142 . This PR enables decoding and encoding support for SAM/BAM files containing CIGARs with operation longer than 65535 operations. According to [Sequence Alignment/Map Format Specification](http://samtools.github.io/hts-specs/SAMv1.pdf), if...
Bumps [xcoo/clj-lint-action](https://github.com/xcoo/clj-lint-action) from 1.1.10 to 1.1.11. Release notes Sourced from xcoo/clj-lint-action's releases. v1.1.11 What's Changed Use the latest eastwood for leiningen projects by @alumi in xcoo/clj-lint-action#3 Add support for eastwood-arguments....
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Detect CIGARs like `kSmN` and refer to `CG` tags.
A bgzipped VCF file over HTTP causes infinite loop. ```console $ gzip -c test-resources/vcf/test-v4_3.vcf > test-resources/vcf/test-v4_3-gzip.vcf.gz $ bgzip -c test-resources/vcf/test-v4_3.vcf > test-resources/vcf/test-v4_3-bgzip.vcf.gz $ python3 -m http.server 8000 ``` ```clj (require...
This is a neat clojure library for bioinformatics. Do you plan on adding [CRAM][0] file support? [0]: https://samtools.github.io/hts-specs/CRAMv3.pdf
#### input SAM ``` @SQ SN:ref LN:45 q001 0 ref 10 60 4I4M4D4M4I * 0 0 ATGCATGCATGCATGC ABCDEFGHIJKLMNOP ``` #### samtools output ``` ref 10 N 1 ^]A E ref...
Currently, the VCF reader/writer aren't supporting `##META` meta info line, which is [mentioned in the spec v4.3](https://github.com/samtools/hts-specs/blob/ce7f2a61fca5e9f906caa72128cade0065b8361a/VCFv4.3.tex#L233-L236). They don't throw an error when encountering such lines, but silently process them...
CIGAR code with adjacent indels (e.g. 1M2D3I, 1M2N3I) is allowed by [SAM file format specification](https://github.com/samtools/hts-specs/blob/a38e257ca855a9693737c85bc22c7689be49fdf4/SAMv1.tex#L358). Insertions and deletions are piled up at the base position just before them according to...
I removed CLI functionality from cljam and added a notice message about [Gnife](https://github.com/chrovis/gnife) to `README.md`. This PR aims at separating the CLI functionality from cljam and making cljam a pure...