4 local curcontext="$curcontext" state line ret=1
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 redistrubute 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.]" \