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#!/bin/sh -e
pkg=last-align
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/examples/*.fa* .
gunzip -r *
# first example from tutorial
lastdb -cR01 humdb humanMito.fa
lastal humdb fuguMito.fa > myalns.maf
# multiMito example
lastdb -c humanMito humanMito.fa
lastal -e25 -j4 humanMito mouseMito.fa | last-split | maf-sort > hm.maf
lastal -e25 -j4 humanMito chickenMito.fa | last-split | maf-sort > hc.maf
lastal -e25 -j4 humanMito fuguMito.fa | last-split | maf-sort > hf.maf
maf-join hm.maf hc.maf hf.maf > out
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