e701fa49e7
* Add first impl of samtools autocompletion * Just autocomplete with files all the time * Add init impl of bedtools completion * Add readme.md for bedtools plugin * Add readme for samtools Co-authored-by: Rolf Schroeder <rolf.schroeder@centogene.com>
65 lines
3.2 KiB
Plaintext
65 lines
3.2 KiB
Plaintext
#compdef bedtools
|
|
#autoload
|
|
|
|
local curcontext="$curcontext" state line ret=1
|
|
local -a _files
|
|
|
|
_arguments -C \
|
|
'1: :->cmds' \
|
|
'2:: :->args' && ret=0
|
|
|
|
case $state in
|
|
cmds)
|
|
_values "bedtools command" \
|
|
"--contact[Feature requests, bugs, mailing lists, etc.]" \
|
|
"--help[Print this help menu.]" \
|
|
"--version[What version of bedtools are you using?.]" \
|
|
"annotate[Annotate coverage of features from multiple files.]" \
|
|
"bamtobed[Convert BAM alignments to BED (& other) formats.]" \
|
|
"bamtofastq[Convert BAM records to FASTQ records.]" \
|
|
"bed12tobed6[Breaks BED12 intervals into discrete BED6 intervals.]" \
|
|
"bedpetobam[Convert BEDPE intervals to BAM records.]" \
|
|
"bedtobam[Convert intervals to BAM records.]" \
|
|
"closest[Find the closest, potentially non-overlapping interval.]" \
|
|
"cluster[Cluster (but don't merge) overlapping/nearby intervals.]" \
|
|
"complement[Extract intervals _not_ represented by an interval file.]" \
|
|
"coverage[Compute the coverage over defined intervals.]" \
|
|
"expand[Replicate lines based on lists of values in columns.]" \
|
|
"fisher[Calculate Fisher statistic b/w two feature files.]" \
|
|
"flank[Create new intervals from the flanks of existing intervals.]" \
|
|
"genomecov[Compute the coverage over an entire genome.]" \
|
|
"getfasta[Use intervals to extract sequences from a FASTA file.]" \
|
|
"groupby[Group by common cols. & summarize oth. cols. (~ SQL "groupBy")]" \
|
|
"igv[Create an IGV snapshot batch script.]" \
|
|
"intersect[Find overlapping intervals in various ways.]" \
|
|
"jaccard[Calculate the Jaccard statistic b/w two sets of intervals.]" \
|
|
"links[Create a HTML page of links to UCSC locations.]" \
|
|
"makewindows[Make interval "windows" across a genome.]" \
|
|
"map[Apply a function to a column for each overlapping interval.]" \
|
|
"maskfasta[Use intervals to mask sequences from a FASTA file.]" \
|
|
"merge[Combine overlapping/nearby intervals into a single interval.]" \
|
|
"multicov[Counts coverage from multiple BAMs at specific intervals.]" \
|
|
"multiinter[Identifies common intervals among multiple interval files.]" \
|
|
"nuc[Profile the nucleotide content of intervals in a FASTA file.]" \
|
|
"overlap[Computes the amount of overlap from two intervals.]" \
|
|
"pairtobed[Find pairs that overlap intervals in various ways.]" \
|
|
"pairtopair[Find pairs that overlap other pairs in various ways.]" \
|
|
"random[Generate random intervals in a genome.]" \
|
|
"reldist[Calculate the distribution of relative distances b/w two files.]" \
|
|
"sample[Sample random records from file using reservoir sampling.]" \
|
|
"shuffle[Randomly redistrubute intervals in a genome.]" \
|
|
"slop[Adjust the size of intervals.]" \
|
|
"sort[Order the intervals in a file.]" \
|
|
"subtract[Remove intervals based on overlaps b/w two files.]" \
|
|
"tag[Tag BAM alignments based on overlaps with interval files.]" \
|
|
"unionbedg[Combines coverage intervals from multiple BEDGRAPH files.]" \
|
|
"window[Find overlapping intervals within a window around an interval.]" \
|
|
ret=0
|
|
;;
|
|
*)
|
|
_files
|
|
;;
|
|
esac
|
|
|
|
return ret
|