diff --git a/cli.c b/cli.c index c1e8216..5238246 100644 --- a/cli.c +++ b/cli.c @@ -182,7 +182,7 @@ int main(int argc, char *argv[]) ksw_extz_t ez; gzFile fp[2]; - while ((c = getopt(argc, argv, "t:w:R:e:rscxvgz:A:B:O:E:Ka")) >= 0) { + while ((c = getopt(argc, argv, "t:w:R:e:rscxvgqz:A:B:O:E:Ka")) >= 0) { if (c == 't') algo = optarg; else if (c == 'w') w = atoi(optarg); else if (c == 'R') rep = atoi(optarg); @@ -194,6 +194,7 @@ int main(int argc, char *argv[]) else if (c == 'x') flag |= KSW_EZ_EXTZ_ONLY; else if (c == 'v') flag |= KSW_EZ_REV_CIGAR; else if (c == 'g') flag |= KSW_EZ_APPROX_MAX | KSW_EZ_APPROX_DROP; + else if (c == 'q') flag |= KSW_EZ_EQX; else if (c == 'K') no_kalloc = 1; else if (c == 'A') a = atoi(optarg); else if (c == 'B') b = atoi(optarg); diff --git a/coverage.sh b/coverage.sh index ee62d6b..1d0a9c9 100755 --- a/coverage.sh +++ b/coverage.sh @@ -3,7 +3,7 @@ if [ -z "$KSW2COV" ]; then KSW2COV=./ksw2-test fi -# Test code coverage of ksw2 +# Test code coverage of ksw2 u=$1 t=$2 @@ -13,14 +13,21 @@ $KSW2COV $u $t ${@:2} # Enables KSW_EZ_RIGHT $KSW2COV $u $t -r ${@:2} -## Enables KSW_EZ_GENERIC_SC -$KSW2COV $u $t -c ${@:2} +## Enables KSW_EZ_GENERIC_SC +$KSW2COV $u $t -c ${@:2} -# Enables KSW_EZ_REV_CIGAR -$KSW2COV $u $t -v ${@:2} +# Enables KSW_EZ_REV_CIGAR +$KSW2COV $u $t -v ${@:2} -# Enables KSW_EZ_EXTZ_ONLY -$KSW2COV $u $t -x ${@:2} +# Enables KSW_EZ_EXTZ_ONLY +$KSW2COV $u $t -x ${@:2} + +# Enables KSW_EZ_APPROX_MAX +$KSW2COV $u $t -g ${@:2} + +# Enables KSW_EZ_EQX +# This option is disabled because the baseline kernel segmentation faults with this option enabled +# $KSW2COV $u $t -q ${@:2} # Sets end_bonus and zdrop $KSW2COV $u $t ${@:2} -x -e 1 -z 1