_samtools

#compdef samtools

# Usage:   samtools <command> [options]
# see _samtools way below for the entrypoint



_samtools-collate() {
	local ret=1
	local -a args
	args+=(
		'-O[output to stdout]'
		'-u[uncompressed BAM output]'
		'-l+[compression level; default: 1]:int:'
		'-n+[number of temporary files; default: 64]:int:'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-bedcov() {
	_arguments '*:files:_files'
	return 0
}

_samtools-calmd() {
	local ret=1
	local -a args
	args+=(
		# FIXME
		# my version of samtools outputs the help for fillmd‽
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-cat() {
	local ret=1
	local -a args
	args+=(
		'-h+[-h header.sam]:file:_files'
		'-o+[-o out.bam]:file:_files'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-depth() {
	local ret=1
	local -a args
	args+=(
		'-b+[list of positions or regions]:bed:_files'
		'-f+[list of input BAM filenames, one per line]:list:_files'
		'-l+[minQLen]:int:'
		'-q+[base quality threshold]:int:'
		'-Q+[mapping quality threshold]:int:'
		'-r+[chr:from-to]:region:'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-faidx() {
	_arguments '*:files:_files'
	return 0
}

_samtools-fixmate() {
	local ret=1
	local -a args
	args+=(
		'-r[remove unmapped reads and secondary alignments]'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-flagstat() {
	_arguments '*:files:_files'
	return 0
}

_samtools-idxstats() {
	_arguments '*:files:_files'
	return 0
}

_samtools-index() {
	_arguments '*:files:_files'
	return 0
}

_samtools-merge() {
	local ret=1
	local -a args
	args+=(
		'-1[compress level 1]'
		'-@[number of BAM compression thread]:int:'
		'-f[overwrite the output BAM if exist]'
		'-h[copy the header in FILE to <out.bam>]:FILE:_files'
		'-l+[compression level, from 0 to 9]:int:'
		'-n[sort by read names]'
		'-r[attach RG tag (inferred from file names)]'
		'-R+[merge file in the specified region]:str:'
		'-u[uncompressed BAM output]'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-mpileup() {
	_arguments '*:files:_files'
	return 0
}

_samtools-phase() {
	local ret=1
	local -a args
	args+=(
		'-A[drop reads with ambiguous phase]'
		'-b+[prefix of BAMs to output (default: null)]:str:'
		'-D+[max read depth (default: 256)]:int:'
		'-F[do not attempt to fix chimeras]'
		'-k+[block length (default: 13)]:int:'
		'-Q+[min base quality in het calling (default: 13)]:int:'
		'-q+[min het phred-LOD (default: 37)]:int:'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-reheader() {
	_arguments '*:files:_files'
	return 0
}

_samtools-rmdup() {
	local ret=1
	local -a args
	args+=(
		'-s[rmdup for SE reads]'
		'-S[treat PE reads as SE]'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-sort() {
	local ret=1
	local -a args
	args+=(
		'-@[number of sorting and compression thread (default: 1)]:int:'
		'-f[use <out.prefix> as full file name instead of prefix]'
		'-l+[compression level, from 0 to 9 (default: -1)]:int:'
		'-m+[max memory per thread; suffix K/M/G recognize (default: 768M)]:int:'
		'-n[sort by read name]'
		'-t[sort by value of TAG, uses position as secondary index (or read name if -n is set)]:str:'
		'-o+[write final output to FILE]:files:_files'
		'-O+[output format]:str:(SAM BAM CRAM)'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-targetcut() {
	local ret=1
	local -a args
	args+=(
		'-0+[-0 em0]:em0:'
		'-1+[-1 em1]:em1:'
		'-2+[-2 em2]:em2:'
		'-f+[-f ref]:ref:'
		'-i+[-i inPen]:inPen:'
		'-Q+[-Q minQ]:minQ:'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-tview() {
	local ret=1
	local -a args
	args+=(
		'-d+[output format]:display:((
			C\:Curses
			H\:Html
			T\:Text
		))'
		'-p+[got directly to this position]:chr pos:'
		'-s+[display only reads from this sample or group]:str:'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	return ret
}

_samtools-view() {
	local ret=1
	local -a args
	args+=(
		'-1[fast compression (force -b)]'
		'-?[longer help]'
		'-@[number of BAM compression threads (default: 0)]:int:'
		'-B[collapse the backward CIGAR operation]'
		'-b[output BAM]'
		'-c[print only the count of matching records]'
		'-C[output CRAM (requires -T)]'
		'-F+[filtering flag, 0 for unset (default: 0)]:flag:->flags'
		'-f+[required flag, 0 for unset (default: 0)]:flag:->flags'
		'-h[print header for the SAM output]'
		'-H[print header only (no alignments)]'
		'-l+[only output reads in library STR (default: null)]:str:'
		'-L+[output alignments overlapping the input BED FILE (default: null)]:file:_files'
		'-M[use the multi-region iterator]'
		'-N+[output only alignments with read name listed in FILE]:file:_files'
		'-o+[output file name (default: stdout)]:file:_files'
		'-O+[output format]:str:(SAM BAM CRAM)'
		'-P[Retrieve pairs even when the mate is outside of the requested region]'
		'-q+[minimum mapping quality (default: 0)]:int:'
		'-R+[list of read groups to be outputted (default: null)]:file:_files'
		'-r+[only output reads in read group STR (default: null)]:str:'
		'-s+[fraction of templates to subsample; integer part as seed (default: -1)]:float:'
		'-S[input format is auto-detected]'
		'-t+[list of reference names and lengths (force -S) (default: null)]:file:_files'
		'-T+[reference sequence file (default: null)]:file:_files'
		'-u[uncompressed BAM output (force -b)]'
		'-U+[output reads not selected by filters to FILE]:file:_files'
		'-x[read tag to strip]:str:'
		'*:files:_files'
	)
	_arguments -w -s -S $args[@] && ret=0
	case "$state" in
		(flags)
		_values -s , 'flags' unmap munmap secondary supplementary qcfail dup paired proper_pair reverse mreverse read1 read2
		;;
	esac
	return ret
}

_samtools() {
	local ret=1
	local -a args
	if ((CURRENT == 2)); then
		args+=(
			'1:command:((
				# samtools v1.8
				# -- Indexing
				dict:create\ a\ sequence\ dictionary\ file
				faidx:index/extract\ FASTA
				index:index\ alignment
				# -- Editing
				calmd:recalculate\ MD/NM\ tags\ and\ \"=\"\ bases
				fixmate:fix\ mate\ information
				reheader:replace\ BAM\ header
				targetcut:cut\ fosmid\ regions\ \(for\ fosmid\ pool\ only\)
				addreplacerg:adds\ or\ replaces\ RG\ tags
				markdup:mark\ duplicates
				collate:shuffle\ and\ group\ alignments\ by\ name
				cat:concatenate\ BAMs
				merge:merge\ sorted\ alignments
				mpileup:multi\-way\ pileup
				sort:sort\ alignment\ file
				split:splits\ a\ file\ by\ read\ group
				quickcheck:quickly\ check\ if\ SAM/BAM/CRAM\ file\ appears\ intact
				fastq:converts\ a\ BAM\ to\ a\ FASTQ
				fasta:converts\ a\ BAM\ to\ a\ FASTA
				# -- Statistics
				bedcov:read\ depth\ per\ BED\ region
				depth:compute\ the\ depth
				flagstat:simple\ stats
				idxstats:BAM\ index\ stats
				phase:phase\ heterozygotes
				stats:generate\ stats\ \(former\ bamcheck\)
				# -- Viewing
				flags:explain\ BAM\ flags
				tview:text\ alignment\ viewer
				view:SAM\<\-\>BAM\<\-\>CRAM\ conversion
				depad:convert\ padded\ BAM\ to\ unpadded\ BAM
				# deprecated?
				rmdup:remove\ PCR\ duplicates
			))'
			'(- *)--help[Display help message]'
		)
		_arguments $args[@] && ret=0
		return ret
	else
		# delegate to sub commands
		local subcmd=_samtools-$words[2]
		if ! _call_function ret $subcmd ; then
			_message "unknown sub-command: $words[2]"
		fi
		return ret
	fi
}

_samtools