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| author | Aditya <bluenerd@protonmail.com> | 2023-02-27 20:04:56 +0530 |
|---|---|---|
| committer | Aditya <bluenerd@protonmail.com> | 2023-02-27 20:04:56 +0530 |
| commit | edc449275b6c04445f58b108ca0937a87c1e8430 (patch) | |
| tree | 9fd484d58145b616f29a78857cc0b1c8b1c18f05 /oh-my-zsh/plugins/samtools/_samtools | |
| parent | 6f5424ca96c4221ef433f545642669e9c104d0ed (diff) | |
add zsh
Diffstat (limited to 'oh-my-zsh/plugins/samtools/_samtools')
| -rw-r--r-- | oh-my-zsh/plugins/samtools/_samtools | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/oh-my-zsh/plugins/samtools/_samtools b/oh-my-zsh/plugins/samtools/_samtools new file mode 100644 index 0000000..ddb002a --- /dev/null +++ b/oh-my-zsh/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 |