marcelm · December 8, 2015 13:20
diff --git a/bambai b/bambai
 #!/bin/bash
 set -euo pipefail
 if [ $# -ne 1 -o x$1 == x-h -o x$1 == x--help ]; then
    echo \
 "Usage:

    samtools sort -O bam -T prefix ... | bambai BAMPATH

 Read a sorted BAM file from standard input, write it to BAMPATH and
 index it at the same time (creating BAMPATH.bai)."
    exit 2
 fi
 if [ -t 0 ]; then
 	echo "Reading input from terminal - this is probably not what you want. Use Ctrl+C to cancel."
 fi
 BAM="$1"
 WORKDIR=$(mktemp -d) || exit 1
 trap "rm -rf ${WORKDIR}" exit
 FIFO=${WORKDIR}/fifo.bam
 mkfifo ${FIFO}
 samtools index ${FIFO} && mv ${FIFO}.bai "${BAM}.bai" &
 tee ${FIFO} > "${BAM}"
	#!/bin/bash
	set -euo pipefail
	if [ $# -ne 1 -o x$1 == x-h -o x$1 == x--help ]; then
	echo \
	"Usage:

	samtools sort -O bam -T prefix ... \| bambai BAMPATH

	Read a sorted BAM file from standard input, write it to BAMPATH and
	index it at the same time (creating BAMPATH.bai)."
	exit 2
	fi
	if [ -t 0 ]; then
	echo "Reading input from terminal - this is probably not what you want. Use Ctrl+C to cancel."
	fi
	BAM="$1"
	WORKDIR=$(mktemp -d) \|\| exit 1
	trap "rm -rf ${WORKDIR}" exit
	FIFO=${WORKDIR}/fifo.bam
	mkfifo ${FIFO}
	samtools index ${FIFO} && mv ${FIFO}.bai "${BAM}.bai" &
	tee ${FIFO} > "${BAM}"