[med-svn] [Git][med-team/kma][upstream] New upstream version 1.3.8
Nilesh Patra
gitlab at salsa.debian.org
Mon Nov 30 10:21:22 GMT 2020
Nilesh Patra pushed to branch upstream at Debian Med / kma
Commits:
42961940 by Nilesh Patra at 2020-11-30T15:48:17+05:30
New upstream version 1.3.8
- - - - -
3 changed files:
- kma.c
- nw.c
- version.h
Changes:
=====================================
kma.c
=====================================
@@ -540,7 +540,7 @@ int kma_main(int argc, char *argv[]) {
if(++args < argc && *(argv[args]) != '-') {
ref_fsa = strtoul(argv[args], &exeBasic, 10);
if(*exeBasic != 0) {
- fprintf(stderr, "Invalid argument at \"-3p\".\n");
+ fprintf(stderr, "Invalid argument at \"-ref_fsa\".\n");
exit(4);
} else if(ref_fsa == 0) {
ref_fsa = 2;
@@ -785,7 +785,7 @@ int kma_main(int argc, char *argv[]) {
++args;
extendedFeatures = strtol(argv[args], &exeBasic, 10);
if(*exeBasic != 0) {
- fprintf(stderr, "Invalid argument at \"-Mt1\".\n");
+ fprintf(stderr, "Invalid argument at \"-ef\".\n");
exit(1);
}
} else {
@@ -843,6 +843,10 @@ int kma_main(int argc, char *argv[]) {
tmp = 1;
if(++args < argc) {
if(argv[args][0] != '-') {
+ if(argv[args][strlen(argv[args]) - 1] != '/') {
+ fprintf(stderr, "Invalid output directory specified.\n");
+ exit(1);
+ }
tmpF(argv[args]);
tmp = 0;
} else {
@@ -864,6 +868,50 @@ int kma_main(int argc, char *argv[]) {
verbose = 1;
--args;
}
+ } else if(strcmp(argv[args], "-mint2") == 0) {
+ /* equivalent to:
+ -1t1, -mem_mode, -ca, -cge, -mq 1, -ref_fsa 2, -dense,
+ -bcg, -bcd 10, -bc 0.9 -vcf -ef */
+ kmerScan = &save_kmers;
+ one2one = 1;
+ mem_mode = 1;
+ alignLoadPtr = &alignLoad_fly_mem;
+ ankerPtr = &ankerAndClean_MEM;
+ chainSeedsPtr = &chainSeeds_circular;
+ scoreT = 0.75;
+ rewards->M = 1;
+ rewards->MM = -3;
+ rewards->W1 = -5;
+ rewards->U = -1;
+ rewards->PE = 17;
+ mq = 1;
+ ref_fsa = 2;
+ alnToMatPtr = alnToMatDense;
+ baseCall = &orgBaseCaller;
+ bcd = 10;
+ significantBase = &significantAndSupport;
+ significantAndSupport(0, 0, 0.9);
+ vcf = 1;
+ extendedFeatures = 1;
+ } else if(strcmp(argv[args], "-mint3") == 0) {
+ /* equivalent to:
+ -1t1, -mem_mode, -ca, -mq 1, -ref_fsa, -dense,
+ -bcNano, -bcd 10 -bc 0.7 -vcf -ef */
+ kmerScan = &save_kmers;
+ one2one = 1;
+ mem_mode = 1;
+ alignLoadPtr = &alignLoad_fly_mem;
+ ankerPtr = &ankerAndClean_MEM;
+ chainSeedsPtr = &chainSeeds_circular;
+ mq = 1;
+ ref_fsa = 2;
+ alnToMatPtr = alnToMatDense;
+ baseCall = &nanoCaller;
+ bcd = 10;
+ significantBase = &significantAndSupport;
+ significantAndSupport(0, 0, 0.7);
+ vcf = 1;
+ extendedFeatures = 1;
} else if(strcmp(argv[args], "-v") == 0) {
fprintf(stdout, "KMA-%s\n", KMA_VERSION);
exit(0);
=====================================
nw.c
=====================================
@@ -197,7 +197,7 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,
/* Update D, match */
thisScore = D_prev[n + 1] + d[t_nuc][query[n]];
- if(D_ptr[n] < thisScore) {
+ if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
E_ptr[n] |= 1;
} else {
@@ -209,7 +209,7 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,
E_ptr -= (q_len + 1);
- if(k < 0 && Stat.score <= *D_ptr) {
+ if(k < 0 && Stat.score < *D_ptr) {
Stat.score = *D_ptr;
pos[0] = m;
}
@@ -229,7 +229,7 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,
pos[1] = 0;
if(k == -2) {
for(n = 0; n < q_len; ++n) {
- if(D_prev[n] > Stat.score) {
+ if(Stat.score <= D_prev[n]) {
Stat.score = D_prev[n];
pos[0] = 0;
pos[1] = (aligned->start = n);
@@ -486,7 +486,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i
/* Update D, match */
thisScore = D_prev[n] + d[t_nuc][query[q_pos]];
- if(D_ptr[n] < thisScore) {
+ if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
E_ptr[n] |= 1;
} else {
@@ -517,7 +517,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i
D_ptr[n] = D_prev[n] + d[t_nuc][query[q_pos]];
/* set D to max, and set E */
- if(Q < D_ptr[n]) {
+ if(Q <= D_ptr[n]) {
E_ptr[n] |= 1;
} else {
D_ptr[n] = Q;
@@ -527,7 +527,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i
/* continue as usual */
E_ptr -= (bq_len + 1);
- if(eq == 0 && k < 0 && Stat.score <= D_ptr[n]) {
+ if(eq == 0 && k < 0 && Stat.score < D_ptr[n]) {
Stat.score = D_ptr[n];
pos[0] = m;
pos[1] = n;
@@ -551,7 +551,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i
}
if(k == -2) {
for(n = en; n < bq_len; ++n) {
- if(D_prev[n] > Stat.score) {
+ if(Stat.score <= D_prev[n]) {
Stat.score = D_prev[n];
pos[0] = 0;
pos[1] = n;
@@ -776,7 +776,7 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,
/* Update D, match */
thisScore = D_prev[n + 1] + d[t_nuc][query[n]];
- if(D_ptr[n] < thisScore) {
+ if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
E_ptr[n] |= 1;
} else {
@@ -788,7 +788,7 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,
E_ptr -= (q_len + 1);
- if(k < 0 && Stat.score <= *D_ptr) {
+ if(k < 0 && Stat.score < *D_ptr) {
Stat.score = *D_ptr;
pos[0] = m;
}
@@ -808,7 +808,7 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,
pos[1] = 0;
if(k == -2) {
for(n = 0; n < q_len; ++n) {
- if(D_prev[n] > Stat.score) {
+ if(Stat.score <= D_prev[n]) {
Stat.score = D_prev[n];
pos[0] = 0;
pos[1] = n;
@@ -1030,7 +1030,7 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query
/* Update D, match */
thisScore = D_prev[n] + d[t_nuc][query[q_pos]];
- if(D_ptr[n] < thisScore) {
+ if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
E_ptr[n] |= 1;
} else {
@@ -1061,7 +1061,7 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query
D_ptr[n] = D_prev[n] + d[t_nuc][query[q_pos]];
/* set D to max, and set E */
- if(Q < D_ptr[n]) {
+ if(Q <= D_ptr[n]) {
E_ptr[n] |= 1;
} else {
D_ptr[n] = Q;
@@ -1071,7 +1071,7 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query
/* continue as usual */
E_ptr -= (bq_len + 1);
- if(eq == 0 && k < 0 && Stat.score <= D_ptr[n]) {
+ if(eq == 0 && k < 0 && Stat.score < D_ptr[n]) {
Stat.score = D_ptr[n];
pos[0] = m;
pos[1] = n;
@@ -1095,7 +1095,7 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query
}
if(k == -2) {
for(n = en; n < bq_len; ++n) {
- if(D_prev[n] > Stat.score) {
+ if(Stat.score <= D_prev[n]) {
Stat.score = D_prev[n];
pos[0] = 0;
pos[1] = n;
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.3.7"
+#define KMA_VERSION "1.3.8"
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/429619402ea738804f1c7ef8b0354cd982afeffc
--
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/429619402ea738804f1c7ef8b0354cd982afeffc
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