feat(plugins): New plugins for samtools and bedtools (#3574)

* 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>

plugins/bedtools/README.md

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+# Bedtools plugin
+
+This plugin adds support for the [bedtools suite](http://bedtools.readthedocs.org/en/latest/):
+
+* Adds autocomplete options for all bedtools sub commands.

plugins/bedtools/_bedtools

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+#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

plugins/samtools/README.md

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+# Samtools plugin
+
+This plugin adds support for [samtools](http://www.htslib.org/):
+
+* Adds autocomplete options for all samtools sub commands.

plugins/samtools/_samtools

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+#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