_bedtools

 1#compdef bedtools
 2#autoload
 3
 4local curcontext="$curcontext" state line ret=1
 5local -a _files
 6
 7_arguments -C \
 8  '1: :->cmds' \
 9  '2:: :->args' && ret=0
10
11case $state in
12  cmds)
13    _values "bedtools command" \
14        "--contact[Feature requests, bugs, mailing lists, etc.]" \
15        "--help[Print this help menu.]" \
16        "--version[What version of bedtools are you using?.]" \
17        "annotate[Annotate coverage of features from multiple files.]" \
18        "bamtobed[Convert BAM alignments to BED (& other) formats.]" \
19        "bamtofastq[Convert BAM records to FASTQ records.]" \
20        "bed12tobed6[Breaks BED12 intervals into discrete BED6 intervals.]" \
21        "bedpetobam[Convert BEDPE intervals to BAM records.]" \
22        "bedtobam[Convert intervals to BAM records.]" \
23        "closest[Find the closest, potentially non-overlapping interval.]" \
24        "cluster[Cluster (but don't merge) overlapping/nearby intervals.]" \
25        "complement[Extract intervals _not_ represented by an interval file.]" \
26        "coverage[Compute the coverage over defined intervals.]" \
27        "expand[Replicate lines based on lists of values in columns.]" \
28        "fisher[Calculate Fisher statistic b/w two feature files.]" \
29        "flank[Create new intervals from the flanks of existing intervals.]" \
30        "genomecov[Compute the coverage over an entire genome.]" \
31        "getfasta[Use intervals to extract sequences from a FASTA file.]" \
32        "groupby[Group by common cols. & summarize oth. cols. (~ SQL "groupBy")]" \
33        "igv[Create an IGV snapshot batch script.]" \
34        "intersect[Find overlapping intervals in various ways.]" \
35        "jaccard[Calculate the Jaccard statistic b/w two sets of intervals.]" \
36        "links[Create a HTML page of links to UCSC locations.]" \
37        "makewindows[Make interval "windows" across a genome.]" \
38        "map[Apply a function to a column for each overlapping interval.]" \
39        "maskfasta[Use intervals to mask sequences from a FASTA file.]" \
40        "merge[Combine overlapping/nearby intervals into a single interval.]" \
41        "multicov[Counts coverage from multiple BAMs at specific intervals.]" \
42        "multiinter[Identifies common intervals among multiple interval files.]" \
43        "nuc[Profile the nucleotide content of intervals in a FASTA file.]" \
44        "overlap[Computes the amount of overlap from two intervals.]" \
45        "pairtobed[Find pairs that overlap intervals in various ways.]" \
46        "pairtopair[Find pairs that overlap other pairs in various ways.]" \
47        "random[Generate random intervals in a genome.]" \
48        "reldist[Calculate the distribution of relative distances b/w two files.]" \
49        "sample[Sample random records from file using reservoir sampling.]" \
50        "shuffle[Randomly redistribute intervals in a genome.]" \
51        "slop[Adjust the size of intervals.]" \
52        "sort[Order the intervals in a file.]" \
53        "subtract[Remove intervals based on overlaps b/w two files.]" \
54        "tag[Tag BAM alignments based on overlaps with interval files.]" \
55        "unionbedg[Combines coverage intervals from multiple BEDGRAPH files.]" \
56        "window[Find overlapping intervals within a window around an interval.]" \
57    ret=0
58    ;;
59  *)
60    _files
61    ;;
62esac
63
64return ret