Diff
1diff --git a/plugins/bedtools/README.md b/plugins/bedtools/README.md
2new file mode 100644
3index 0000000000000000000000000000000000000000..c4de4e3a90f2bfa689fedec28ba182f8a8691a4c
4--- /dev/null
5+++ b/plugins/bedtools/README.md
6@@ -0,0 +1,5 @@
7+# Bedtools plugin
8+
9+This plugin adds support for the [bedtools suite](http://bedtools.readthedocs.org/en/latest/):
10+
11+* Adds autocomplete options for all bedtools sub commands.
12diff --git a/plugins/bedtools/_bedtools b/plugins/bedtools/_bedtools
13new file mode 100644
14index 0000000000000000000000000000000000000000..ef6c4179afc7125390fb1a0ae96c03f0fb4acb3c
15--- /dev/null
16+++ b/plugins/bedtools/_bedtools
17@@ -0,0 +1,64 @@
18+#compdef bedtools
19+#autoload
20+
21+local curcontext="$curcontext" state line ret=1
22+local -a _files
23+
24+_arguments -C \
25+ '1: :->cmds' \
26+ '2:: :->args' && ret=0
27+
28+case $state in
29+ cmds)
30+ _values "bedtools command" \
31+ "--contact[Feature requests, bugs, mailing lists, etc.]" \
32+ "--help[Print this help menu.]" \
33+ "--version[What version of bedtools are you using?.]" \
34+ "annotate[Annotate coverage of features from multiple files.]" \
35+ "bamtobed[Convert BAM alignments to BED (& other) formats.]" \
36+ "bamtofastq[Convert BAM records to FASTQ records.]" \
37+ "bed12tobed6[Breaks BED12 intervals into discrete BED6 intervals.]" \
38+ "bedpetobam[Convert BEDPE intervals to BAM records.]" \
39+ "bedtobam[Convert intervals to BAM records.]" \
40+ "closest[Find the closest, potentially non-overlapping interval.]" \
41+ "cluster[Cluster (but don't merge) overlapping/nearby intervals.]" \
42+ "complement[Extract intervals _not_ represented by an interval file.]" \
43+ "coverage[Compute the coverage over defined intervals.]" \
44+ "expand[Replicate lines based on lists of values in columns.]" \
45+ "fisher[Calculate Fisher statistic b/w two feature files.]" \
46+ "flank[Create new intervals from the flanks of existing intervals.]" \
47+ "genomecov[Compute the coverage over an entire genome.]" \
48+ "getfasta[Use intervals to extract sequences from a FASTA file.]" \
49+ "groupby[Group by common cols. & summarize oth. cols. (~ SQL "groupBy")]" \
50+ "igv[Create an IGV snapshot batch script.]" \
51+ "intersect[Find overlapping intervals in various ways.]" \
52+ "jaccard[Calculate the Jaccard statistic b/w two sets of intervals.]" \
53+ "links[Create a HTML page of links to UCSC locations.]" \
54+ "makewindows[Make interval "windows" across a genome.]" \
55+ "map[Apply a function to a column for each overlapping interval.]" \
56+ "maskfasta[Use intervals to mask sequences from a FASTA file.]" \
57+ "merge[Combine overlapping/nearby intervals into a single interval.]" \
58+ "multicov[Counts coverage from multiple BAMs at specific intervals.]" \
59+ "multiinter[Identifies common intervals among multiple interval files.]" \
60+ "nuc[Profile the nucleotide content of intervals in a FASTA file.]" \
61+ "overlap[Computes the amount of overlap from two intervals.]" \
62+ "pairtobed[Find pairs that overlap intervals in various ways.]" \
63+ "pairtopair[Find pairs that overlap other pairs in various ways.]" \
64+ "random[Generate random intervals in a genome.]" \
65+ "reldist[Calculate the distribution of relative distances b/w two files.]" \
66+ "sample[Sample random records from file using reservoir sampling.]" \
67+ "shuffle[Randomly redistrubute intervals in a genome.]" \
68+ "slop[Adjust the size of intervals.]" \
69+ "sort[Order the intervals in a file.]" \
70+ "subtract[Remove intervals based on overlaps b/w two files.]" \
71+ "tag[Tag BAM alignments based on overlaps with interval files.]" \
72+ "unionbedg[Combines coverage intervals from multiple BEDGRAPH files.]" \
73+ "window[Find overlapping intervals within a window around an interval.]" \
74+ ret=0
75+ ;;
76+ *)
77+ _files
78+ ;;
79+esac
80+
81+return ret
82diff --git a/plugins/samtools/README.md b/plugins/samtools/README.md
83new file mode 100644
84index 0000000000000000000000000000000000000000..f4baf41f78f0dd96a095bd8ebba086c25e062c49
85--- /dev/null
86+++ b/plugins/samtools/README.md
87@@ -0,0 +1,5 @@
88+# Samtools plugin
89+
90+This plugin adds support for [samtools](http://www.htslib.org/):
91+
92+* Adds autocomplete options for all samtools sub commands.
93diff --git a/plugins/samtools/_samtools b/plugins/samtools/_samtools
94new file mode 100644
95index 0000000000000000000000000000000000000000..ddb002ae273277a99a261e01650d745e249f2b8b
96--- /dev/null
97+++ b/plugins/samtools/_samtools
98@@ -0,0 +1,40 @@
99+#compdef samtools
100+#autoload
101+
102+local curcontext="$curcontext" state line ret=1
103+local -a _files
104+
105+_arguments -C \
106+ '1: :->cmds' \
107+ '2:: :->args' && ret=0
108+
109+case $state in
110+ cmds)
111+ _values "samtools command" \
112+ "view[SAM<->BAM conversion]" \
113+ "sort[sort alignment file]" \
114+ "mpileup[multi-way pileup]" \
115+ "depth[compute the depth]" \
116+ "faidx[index/extract FASTA]" \
117+ "tview[text alignment viewer]" \
118+ "index[index alignment]" \
119+ "idxstats[BAM index stats (r595 or later)]" \
120+ "fixmate[fix mate information]" \
121+ "flagstat[simple stats]" \
122+ "calmd[recalculate MD/NM tags and '=' bases]" \
123+ "merge[merge sorted alignments]" \
124+ "rmdup[remove PCR duplicates]" \
125+ "reheader[replace BAM header]" \
126+ "cat[concatenate BAMs]" \
127+ "bedcov[read depth per BED region]" \
128+ "targetcut[cut fosmid regions (for fosmid pool only)]" \
129+ "phase[phase heterozygotes]" \
130+ "bamshuf[shuffle and group alignments by name]"
131+ ret=0
132+ ;;
133+ *)
134+ _files
135+ ;;
136+esac
137+
138+return ret