[med-svn] [Git][med-team/kma][upstream] New upstream version 1.4.11
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sun Jan 29 09:39:53 GMT 2023
Nilesh Patra pushed to branch upstream at Debian Med / kma
Commits:
79d1c6be by Nilesh Patra at 2023-01-29T15:05:19+05:30
New upstream version 1.4.11
- - - - -
4 changed files:
- alnfrags.c
- updatescores.c
- updatescores.h
- version.h
Changes:
=====================================
alnfrags.c
=====================================
@@ -1077,7 +1077,6 @@ int alnFragsSE(HashMapCCI **templates_index, int *matched_templates, int *templa
Wl = -NWmatrices->rewards->Wl;
arc = points->len;
points->len = 0;
-
for(t_i = 1; t_i <= *matched_templates; ++t_i) {
template = matched_templates[t_i];
/* check if index DB is loaded */
@@ -1207,8 +1206,8 @@ int alnFragsSE(HashMapCCI **templates_index, int *matched_templates, int *templa
if(*best_read_score > kmersize) {
lock(excludeOut);
- //update_Scores(qseq, q_len, minFrac, bestHits, *best_read_score, bestLen, best_start_pos, best_end_pos, bestTemplates, Scores, Lengths, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
- update_Scores(qseq, q_len, minFrac, bestHits, *best_read_score, bestScore, best_start_pos, best_end_pos, bestTemplates, Scores, Lengths, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ //*matched_templates = update_Scores(qseq, q_len, minFrac, bestHits, *best_read_score, bestLen, best_start_pos, best_end_pos, bestTemplates, Scores, Lengths, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores(qseq, q_len, minFrac, bestHits, *best_read_score, bestScore, best_start_pos, best_end_pos, bestTemplates, Scores, Lengths, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
return 0;
} else {
@@ -1432,7 +1431,7 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t
bestTemplates[t_i] = -bestTemplates[t_i];
}
lock(excludeOut);
- update_Scores_pe(qseq_r, qseq_r_comp->seqlen, qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score + *best_read_score_r, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, header, *flag_r, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_pe(qseq_r, qseq_r_comp->seqlen, qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score + *best_read_score_r, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, header, *flag_r, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
} else {
if(!rc) {
@@ -1442,7 +1441,7 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t
*flag_r ^= 48;
}
lock(excludeOut);
- update_Scores_pe(qseq, qseq_comp->seqlen, qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score + *best_read_score_r, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, header_r, *flag, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_pe(qseq, qseq_comp->seqlen, qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score + *best_read_score_r, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, header_r, *flag, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
}
} else {
@@ -1511,8 +1510,8 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t
bestLen,
Lengths
*/
- update_Scores_se(qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, matched_templates, bestTemplates, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
- update_Scores_se(qseq_r, qseq_r_comp->seqlen, minFrac, bestHits_r, *best_read_score_r, best_start_pos + end, best_end_pos + end, matched_templates + end, bestTemplates_r, header_r, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_se(qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, matched_templates, bestTemplates, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates += update_Scores_se(qseq_r, qseq_r_comp->seqlen, minFrac, bestHits_r, *best_read_score_r, best_start_pos + end, best_end_pos + end, matched_templates + end, bestTemplates_r, header_r, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
}
return 0;
@@ -1547,7 +1546,7 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t
}
lock(excludeOut);
- update_Scores_se(qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_se(qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
return 2;
@@ -1584,7 +1583,7 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t
bestLen,
Lengths
*/
- update_Scores_se(qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score_r, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_se(qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score_r, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
return 1;
@@ -1809,7 +1808,7 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int
bestTemplates[t_i] = -bestTemplates[t_i];
}
lock(excludeOut);
- update_Scores_pe(qseq_r, qseq_r_comp->seqlen, qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, header, *flag_r, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_pe(qseq_r, qseq_r_comp->seqlen, qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, header, *flag_r, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
} else {
if(!rc) {
@@ -1819,7 +1818,7 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int
*flag_r ^= 48;
}
lock(excludeOut);
- update_Scores_pe(qseq, qseq_comp->seqlen, qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, header_r, *flag, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_pe(qseq, qseq_comp->seqlen, qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, header_r, *flag, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
}
return 0;
@@ -1889,8 +1888,8 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int
bestLen,
Lengths
*/
- update_Scores_se(qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, matched_templates, bestTemplates, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
- update_Scores_se(qseq_r, qseq_r_comp->seqlen, minFrac, bestHits_r, *best_read_score_r, best_start_pos + end, best_end_pos + end, matched_templates + end, bestTemplates_r, header_r, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_se(qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, matched_templates, bestTemplates, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates += update_Scores_se(qseq_r, qseq_r_comp->seqlen, minFrac, bestHits_r, *best_read_score_r, best_start_pos + end, best_end_pos + end, matched_templates + end, bestTemplates_r, header_r, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
return 0;
@@ -1925,7 +1924,7 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int
}
lock(excludeOut);
- update_Scores_se(qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_se(qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
return 2;
@@ -1962,7 +1961,7 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int
bestLen,
Lengths
*/
- update_Scores_se(qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score_r, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_se(qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score_r, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
return 1;
@@ -2122,7 +2121,7 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t
bestTemplates[t_i] = -bestTemplates[t_i];
}
lock(excludeOut);
- update_Scores_pe(qseq_r, qseq_r_comp->seqlen, qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, header, *flag_r, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_pe(qseq_r, qseq_r_comp->seqlen, qseq, qseq_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header_r, header, *flag_r, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
} else {
/* get rc flag */
@@ -2139,7 +2138,7 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t
*flag_r ^= 48;
}
lock(excludeOut);
- update_Scores_pe(qseq, qseq_comp->seqlen, qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, header_r, *flag, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
+ *matched_templates = update_Scores_pe(qseq, qseq_comp->seqlen, qseq_r, qseq_r_comp->seqlen, minFrac, bestHits, *best_read_score, best_start_pos, best_end_pos, bestTemplates, bestTemplates_r, header, header_r, *flag, *flag_r, alignment_scores, uniq_alignment_scores, frag_out_raw);
unlock(excludeOut);
}
return 0;
=====================================
updatescores.c
=====================================
@@ -200,7 +200,7 @@ void update_Scores_nanoold(unsigned char *qseq, int q_len, double minFrac, int c
sfwrite(bestTemplates, sizeof(int), counter, frag_out_raw);
}
-void update_Scores(unsigned char *qseq, int q_len, double minFrac, int counter, int bestReadScore, double bestScore, int *start, int *end, int *templates, int *Scores, int *Lengths, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw) {
+int update_Scores(unsigned char *qseq, int q_len, double minFrac, int counter, int bestReadScore, double bestScore, int *start, int *end, int *templates, int *Scores, int *Lengths, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw) {
int i, score, buffer[5];
int *bestTemplates, *bestStart, *bestEnd;
@@ -251,8 +251,8 @@ void update_Scores(unsigned char *qseq, int q_len, double minFrac, int counter,
}
}
} else {
- minScore = (-minFrac) * bestScore;
- minFrac = (-minFrac) * bestReadScore;
+ minScore = minFrac * bestScore;
+ minFrac = minFrac * bestReadScore;
while(--i) {
score = *++Scores;
if((*++Lengths * minScore <= score) || minFrac <= score) {
@@ -293,9 +293,11 @@ void update_Scores(unsigned char *qseq, int q_len, double minFrac, int counter,
sfwrite(bestStart, sizeof(int), counter, frag_out_raw);
sfwrite(bestEnd, sizeof(int), counter, frag_out_raw);
sfwrite(bestTemplates, sizeof(int), counter, frag_out_raw);
+
+ return counter;
}
-void update_Scores_se(unsigned char *qseq, int q_len, double minFrac, int counter, int bestScore, int *start, int *end, int *templates, int *Scores, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw) {
+int update_Scores_se(unsigned char *qseq, int q_len, double minFrac, int counter, int bestScore, int *start, int *end, int *templates, int *Scores, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw) {
int i, buffer[5];
int *bestTemplates, *bestStart, *bestEnd;
@@ -381,9 +383,11 @@ void update_Scores_se(unsigned char *qseq, int q_len, double minFrac, int counte
sfwrite(bestStart, sizeof(int), counter, frag_out_raw);
sfwrite(bestEnd, sizeof(int), counter, frag_out_raw);
sfwrite(bestTemplates, sizeof(int), counter, frag_out_raw);
+
+ return counter;
}
-void update_Scores_pe(unsigned char *qseq, int q_len, unsigned char *qseq_r, int qr_len, double minFrac, int counter, int bestScore, int *start, int *end, int *templates, int *Scores, Qseqs *header, Qseqs *header_r, int flag, int flag_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw) {
+int update_Scores_pe(unsigned char *qseq, int q_len, unsigned char *qseq_r, int qr_len, double minFrac, int counter, int bestScore, int *start, int *end, int *templates, int *Scores, Qseqs *header, Qseqs *header_r, int flag, int flag_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw) {
int i, score, buffer[5];
int *bestTemplates, *bestStart, *bestEnd;
@@ -479,6 +483,8 @@ void update_Scores_pe(unsigned char *qseq, int q_len, unsigned char *qseq_r, int
sfwrite(buffer, sizeof(int), 3, frag_out_raw);
sfwrite(qseq_r, 1, qr_len, frag_out_raw);
sfwrite(header_r->seq, 1, header_r->len, frag_out_raw);
+
+ return counter;
}
void update_Scores_old(unsigned char *qseq, int q_len, int counter, int score, int *start, int *end, int *template, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw) {
=====================================
updatescores.h
=====================================
@@ -22,8 +22,8 @@
void update_Scores_MEM(unsigned char *qseq, int q_len, int counter, int score, int *start, int *end, int *template, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
void update_Scores_pe_MEM(unsigned char *qseq, int q_len, unsigned char *qseq_r, int qr_len, int counter, int score, int *start, int *end, int *template, Qseqs *header, Qseqs *header_r, int flag, int flag_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
-void update_Scores(unsigned char *qseq, int q_len, double minFrac, int counter, int bestReadScore, double bestScore, int *start, int *end, int *templates, int *Scores, int *Lengths, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
-void update_Scores_se(unsigned char *qseq, int q_len, double minFrac, int counter, int bestScore, int *start, int *end, int *templates, int *Scores, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
-void update_Scores_pe(unsigned char *qseq, int q_len, unsigned char *qseq_r, int qr_len, double minFrac, int counter, int bestScore, int *start, int *end, int *templates, int *Scores, Qseqs *header, Qseqs *header_r, int flag, int flag_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
+int update_Scores(unsigned char *qseq, int q_len, double minFrac, int counter, int bestReadScore, double bestScore, int *start, int *end, int *templates, int *Scores, int *Lengths, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
+int update_Scores_se(unsigned char *qseq, int q_len, double minFrac, int counter, int bestScore, int *start, int *end, int *templates, int *Scores, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
+int update_Scores_pe(unsigned char *qseq, int q_len, unsigned char *qseq_r, int qr_len, double minFrac, int counter, int bestScore, int *start, int *end, int *templates, int *Scores, Qseqs *header, Qseqs *header_r, int flag, int flag_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
void update_Scores_old(unsigned char *qseq, int q_len, int counter, int score, int *start, int *end, int *template, Qseqs *header, int flag, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
void update_Scores_pe_old(unsigned char *qseq, int q_len, unsigned char *qseq_r, int qr_len, int counter, int score, int *start, int *end, int *template, Qseqs *header, Qseqs *header_r, int flag, int flag_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, FILE *frag_out_raw);
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.4.10"
+#define KMA_VERSION "1.4.11"
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/79d1c6be10a06c8ac2a069a8d31177261024f9fb
--
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/79d1c6be10a06c8ac2a069a8d31177261024f9fb
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