[med-svn] [Git][med-team/kma][upstream] New upstream version 1.4.3

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch upstream at Debian Med / kma


Commits:
7da40693 by Nilesh Patra at 2022-06-26T00:50:45+05:30
New upstream version 1.4.3
- - - - -


4 changed files:

- alnfrags.c
- kma.c
- tsv.c
- version.h


Changes:

=====================================
alnfrags.c
=====================================
@@ -1151,7 +1151,7 @@ int alnFragsSE(HashMapCCI **templates_index, int *matched_templates, int *templa
 			if(end == t_len) {
 				read_score += Wl;
 			}
-			score = aln_len;//q_len < t_len ? q_len : t_len;
+			score = q_len < t_len ? q_len : t_len;
 		}
 		//read_score += (((start != 0) + (end != template_lengths[abs(template)])) * Wl);
 		


=====================================
kma.c
=====================================
@@ -1116,8 +1116,10 @@ int kma_main(int argc, char *argv[]) {
 				/* -mrc 0.1 */
 				mrc = 0.1;
 				/* -apm p */
+				/*
 				alnFragsPE = &alnFragsPenaltyPE;
 				save_kmers_pair = &save_kmers_penaltyPair;
+				*/
 				/* -lc */
 				kmerAnkerScore = &ankerScoreLen;
 				testExtension = &testExtensionScoreLen;


=====================================
tsv.c
=====================================
@@ -25,6 +25,9 @@
 
 void initsv(FILE *outfile, long unsigned flag) {
 	
+	/* mask off invalid flags */
+	flag &= 65535;
+	
 	printsvField(flag, outfile, "%s%c", "Template_Name");
 	printsvField(flag, outfile, "%s%c", "Template_Length");
 	printsvField(flag, outfile, "%s%c", "Template_Identity");
@@ -47,6 +50,9 @@ void printsv(FILE *outfile, long unsigned flag, char *template_name, Assem *alig
 	
 	//printsv(tsv_out, tsv, template_name, aligned_assem, t_len, readCount, read_score, expected, q_value, p_value, alignment_scores[template]);
 	
+	/* mask off invalid flags */
+	flag &= 65535;
+	
 	/* 0 no file */
 	if(!flag) {
 		return;


=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
  * limitations under the License.
 */
 
-#define KMA_VERSION "1.4.2"
+#define KMA_VERSION "1.4.3"



View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/7da40693c0a28fd25aee61476e110db16406580e

-- 
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/7da40693c0a28fd25aee61476e110db16406580e
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