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#!/bin/bash
set -e
pkg=samclip
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
samclip --ref test.fna < test.sam > out.sam
#samclip --ref ref.fa in1.sam in2.sam > out.sam
# the -h is to emsure the SAM header is included
# samtools view -h in.bam | samclip --ref ref.fa | samtools sort > out.bam
# bwa mem ref.fa R1.fq R2.fq | samclip --ref ref.fa | samtools sort > out.bam.
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