...
 
Commits (2)
......@@ -2,13 +2,13 @@
set -e
VERSION=0.2
VERSION=0.2.1
reference="$1"
query="$2"
unset tmpdir
tmpdir=$(mktemp --tmpdir -d biodiff.XXXX)
tmpdir=$(mktemp -p /tmp -d biodiff.XXXX)
refdir="$tmpdir/ref"
qrydir="$tmpdir/qry"
......@@ -33,6 +33,8 @@ while(<>) {
if ( $_ =~ /^>\s*(\S+)/) {
close($filename);
open($filename, '>', "$ENV{'outdir'}/$1");
} elsif ($_ =~ /^\s*$/) {
next;
} else {
print $filename join("\n", split('', $_))."\n";
}
......@@ -73,10 +75,5 @@ cat <<EOF
#CHROM POS ID REF ALT QUAL FILTER INFO
EOF
diff --ignore-case \
--recursive \
--unified=1 \
--minimal \
--ignore-blank-lines \
"$refdir" "$qrydir" \
diff -irdb -U1 "$refdir" "$qrydir" \
| udiff2vcf
AC_INIT([biodiff],[0.2.0],[aelghraoui@sdsu.edu])
AC_INIT([biodiff],[0.2.1],[aelghraoui@sdsu.edu])
AC_PATH_PROG([DIFF], [diff])
AC_PATH_PROG([PERL], [perl])
AC_PATH_PROG([BCFTOOLS], [bcftools])
......