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Add non-SIMD version of the extd2 kernel. #7

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Add non-SIMD version of the extd2 kernel. #7

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c9ea792
Add non-SIMD version of the extd2 kernel.
ooreilly Oct 24, 2022
c5acd20
Improve code coverage.
ooreilly Oct 27, 2022
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6 changes: 5 additions & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ CPPFLAGS= -g -Wall -Wextra -O2 #-DHAVE_KALLOC
INCLUDES= -I.
OBJS= ksw2_gg.o ksw2_gg2.o ksw2_gg2_sse.o ksw2_extz.o ksw2_extz2_sse.o \
ksw2_extd.o ksw2_extd2_sse.o ksw2_extf2_sse.o ksw2_exts2_sse.o \
ksw2_extd2.o ksw2_extd2_cpp.o
ksw2_extd2.o ksw2_extd2_cpp.o ksw2_extd2_no_sse.o
PROG= ksw2-test
LIBS= -lz
coverage = n
Expand Down Expand Up @@ -63,6 +63,9 @@ report:

ksw2-test:cli.o kalloc.o $(OBJS)
$(CXX) $(CFLAGS) $^ -o $@ $(LIBS_MORE) $(LIBS)

test_vector: test_vector.o
$(CXX) $(CFLAGS) -Wno-incompatible-pointer-types $^ -o [email protected] $(LIBS_MORE) $(LIBS)

clean:
rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM session*
Expand All @@ -78,6 +81,7 @@ kalloc.o: kalloc.h
ksw2_extd.o: ksw2.h
ksw2_extd2_sse.o: ksw2.h
ksw2_extf2_sse.o: ksw2.h
ksw2_extd2_no_sse.o: ksw2.h vector.h
ksw2_extz.o: ksw2.h
ksw2_extz2_sse.o: ksw2.h
ksw2_gg.o: ksw2.h
Expand Down
4 changes: 3 additions & 1 deletion cli.c
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Expand Up @@ -78,6 +78,7 @@ static void global_aln(const char *algo, void *km, const char *qseq_, const char
else if (strcmp(algo, "extz2_sse") == 0) ksw_extz2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, zdrop, 0, flag, ez);
else if (strcmp(algo, "extd") == 0) ksw_extd(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, q2, e2, w, zdrop, flag, ez);
else if (strcmp(algo, "extd2_sse") == 0) ksw_extd2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
else if (strcmp(algo, "extd2_no_sse") == 0) ksw_extd2_no_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
// NOTE: add our c version of alignment
else if (strcmp(algo, "extd2") == 0)
ksw_extd2_c(km, qlen, (uint8_t *)qseq, tlen, (uint8_t *)tseq, m, mat, q,
Expand Down Expand Up @@ -181,7 +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);
Expand All @@ -193,6 +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);
Expand Down
23 changes: 15 additions & 8 deletions coverage.sh
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Expand Up @@ -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

Expand All @@ -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
Expand All @@ -29,4 +36,4 @@ $KSW2COV $u $t ${@:2} -x -e 1 -z 1
$KSW2COV $u $t -s ${@:2}

# Modify the gap penalty to trigger long thres
$KSW2COV -t extd2_cpp $u $t -x -E 2
$KSW2COV $u $t -x -E 2 ${@:2}
3 changes: 3 additions & 0 deletions ksw2.h
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Expand Up @@ -70,6 +70,9 @@ void ksw_extd(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t
void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);

void ksw_extd2_no_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);

void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez);

Expand Down
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