[med-svn] [Git][med-team/kma][master] 3 commits: New upstream version 1.4.11

Nilesh Patra (@nilesh) gitlab at salsa.debian.org
Sun Jan 29 09:39:41 GMT 2023



Nilesh Patra pushed to branch master at Debian Med / kma


Commits:
79d1c6be by Nilesh Patra at 2023-01-29T15:05:19+05:30
New upstream version 1.4.11
- - - - -
b3bad021 by Nilesh Patra at 2023-01-29T15:05:20+05:30
Update upstream source from tag 'upstream/1.4.11'

Update to upstream version '1.4.11'
with Debian dir e2245c7d42d0cd4fa515e2bf53246e76d553e1f3
- - - - -
836d384b by Nilesh Patra at 2023-01-29T15:05:40+05:30
Upload to unstable

- - - - -


5 changed files:

- alnfrags.c
- debian/changelog
- 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;


=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+kma (1.4.11-1) unstable; urgency=medium
+
+  * Team Upload.
+  * New upstream version 1.4.11
+
+ -- Nilesh Patra <nilesh at debian.org>  Sun, 29 Jan 2023 15:05:28 +0530
+
 kma (1.4.10-1) unstable; urgency=medium
 
   * Team upload.


=====================================
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/-/compare/27b21a9a1cd4d0f026f752a3ae77cfeec4760e7b...836d384bb7410ed9a4e3439bf4a198e891378972

-- 
View it on GitLab: https://salsa.debian.org/med-team/kma/-/compare/27b21a9a1cd4d0f026f752a3ae77cfeec4760e7b...836d384bb7410ed9a4e3439bf4a198e891378972
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