4 local curcontext="$curcontext" state line ret=1
13 _values "samtools command" \
14 "view[SAM<->BAM conversion]" \
15 "sort[sort alignment file]" \
16 "mpileup[multi-way pileup]" \
17 "depth[compute the depth]" \
18 "faidx[index/extract FASTA]" \
19 "tview[text alignment viewer]" \
20 "index[index alignment]" \
21 "idxstats[BAM index stats (r595 or later)]" \
22 "fixmate[fix mate information]" \
23 "flagstat[simple stats]" \
24 "calmd[recalculate MD/NM tags and '=' bases]" \
25 "merge[merge sorted alignments]" \
26 "rmdup[remove PCR duplicates]" \
27 "reheader[replace BAM header]" \
28 "cat[concatenate BAMs]" \
29 "bedcov[read depth per BED region]" \
30 "targetcut[cut fosmid regions (for fosmid pool only)]" \
31 "phase[phase heterozygotes]" \
32 "bamshuf[shuffle and group alignments by name]"