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| author | Tuowen Zhao <ztuowen@gmail.com> | 2021-07-11 19:58:51 -0600 |
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| committer | Tuowen Zhao <ztuowen@gmail.com> | 2021-07-11 19:58:51 -0600 |
| commit | 617ed3bd9f3d9519fe2354941f3dbf15b0c712ee (patch) | |
| tree | caf617b35d3f5f7b5786483eedfcda9361dca108 /plugins/samtools | |
| parent | 0144641b7d8e4e6ff6ce153039b5a827f5347904 (diff) | |
| parent | 36f444ed7325720ec05f182781ec7d6c9a4d675c (diff) | |
| download | zsh-617ed3bd9f3d9519fe2354941f3dbf15b0c712ee.tar.gz zsh-617ed3bd9f3d9519fe2354941f3dbf15b0c712ee.tar.bz2 zsh-617ed3bd9f3d9519fe2354941f3dbf15b0c712ee.zip | |
Merge remote-tracking branch 'origin/master'
Diffstat (limited to 'plugins/samtools')
| -rw-r--r-- | plugins/samtools/README.md | 5 | ||||
| -rw-r--r-- | plugins/samtools/_samtools | 40 |
2 files changed, 45 insertions, 0 deletions
diff --git a/plugins/samtools/README.md b/plugins/samtools/README.md new file mode 100644 index 000000000..f4baf41f7 --- /dev/null +++ b/plugins/samtools/README.md @@ -0,0 +1,5 @@ +# Samtools plugin + +This plugin adds support for [samtools](http://www.htslib.org/): + +* Adds autocomplete options for all samtools sub commands. diff --git a/plugins/samtools/_samtools b/plugins/samtools/_samtools new file mode 100644 index 000000000..ddb002ae2 --- /dev/null +++ b/plugins/samtools/_samtools @@ -0,0 +1,40 @@ +#compdef samtools +#autoload + +local curcontext="$curcontext" state line ret=1 +local -a _files + +_arguments -C \ + '1: :->cmds' \ + '2:: :->args' && ret=0 + +case $state in + cmds) + _values "samtools command" \ + "view[SAM<->BAM conversion]" \ + "sort[sort alignment file]" \ + "mpileup[multi-way pileup]" \ + "depth[compute the depth]" \ + "faidx[index/extract FASTA]" \ + "tview[text alignment viewer]" \ + "index[index alignment]" \ + "idxstats[BAM index stats (r595 or later)]" \ + "fixmate[fix mate information]" \ + "flagstat[simple stats]" \ + "calmd[recalculate MD/NM tags and '=' bases]" \ + "merge[merge sorted alignments]" \ + "rmdup[remove PCR duplicates]" \ + "reheader[replace BAM header]" \ + "cat[concatenate BAMs]" \ + "bedcov[read depth per BED region]" \ + "targetcut[cut fosmid regions (for fosmid pool only)]" \ + "phase[phase heterozygotes]" \ + "bamshuf[shuffle and group alignments by name]" + ret=0 + ;; + *) + _files + ;; +esac + +return ret |