[med-svn] [Git][med-team/kma][upstream] New upstream version 1.2.21

[Steffen Möller]

Steffen Möller pushed to branch upstream at Debian Med / kma


Commits:
1e63c095 by Steffen Moeller at 2020-01-17T23:29:15+01:00
New upstream version 1.2.21
- - - - -


6 changed files:

- README.md
- runkma.c
- savekmers.c
- − seqmenttree
- spltdb.c
- version.h


Changes:

=====================================
README.md
=====================================
@@ -24,6 +24,7 @@ BMC Bioinformatics, 2018;19:307.
 
 
 # Usage #
+A more detailed guide on KMA and its options can be found in the pdf "KMAspecification.pdf".
 For practical reasons you might want to add kma to your path, this is usually done with:
 
 ```


=====================================
runkma.c
=====================================
@@ -896,7 +896,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC
 					randScore = tmp_score * tot;
 					
 					score = 0;
-					for(i = 0; i != bestHits; ++i) {
+					for(i = 0; i < bestHits; ++i) {
 						score += uniq_alignment_scores[abs(bestTemplates[i])];
 						if(randScore < score) {
 							bestTemplate = bestTemplates[i];
@@ -1893,7 +1893,6 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
 			
 			/* Several mapped templates, choose best according to sorting keys */
 			if(bestHits != 1) {
-				
 				bestTemplate = 0;
 				bestScore = 0;
 				start = 0;
@@ -1924,7 +1923,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
 					randScore = tmp_score * tot;
 					
 					score = 0;
-					for(i = 0; i != bestHits; ++i) {
+					for(i = 0; i < bestHits; ++i) {
 						score += uniq_alignment_scores[abs(bestTemplates[i])];
 						if(randScore < score) {
 							bestTemplate = bestTemplates[i];
@@ -1996,8 +1995,6 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
 						}
 					}
 				}
-				
-				
 			} else {
 				bestTemplate = *bestTemplates;
 				start = *best_start_pos;
@@ -2070,7 +2067,6 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
 					}
 				}
 			}
-			
 		}
 		template_fragments[fileCount] = printFrags(alignFrags, DB_size);
 		++fileCount;


=====================================
savekmers.c
=====================================
@@ -3568,7 +3568,7 @@ int save_kmers_forcePair(const HashMapKMA *templates, const Penalties *rewards,
 		
 		if((qseq->seqlen + qseq_r->seqlen - bestScore) < bestScore * kmersize) {
 			flag = 67;
-			flag_r = 129;
+			flag_r = 131;
 			
 			if(regionTemplates[*regionTemplates] < 0) {
 				bestScore = -bestScore;


=====================================
seqmenttree deleted
=====================================
Binary files a/seqmenttree and /dev/null differ


=====================================
spltdb.c
=====================================
@@ -1169,7 +1169,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,
 					randScore = tmp_score * tot;
 					
 					score = 0;
-					for(i = 0; i != bestHits; ++i) {
+					for(i = 0; i < bestHits; ++i) {
 						score += uniq_alignment_scores[abs(bestTemplates[i])];
 						if(randScore < score) {
 							bestTemplate = bestTemplates[i];


=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
  * limitations under the License.
 */
 
-#define KMA_VERSION "1.2.19"
+#define KMA_VERSION "1.2.21"



View it on GitLab: https://salsa.debian.org/med-team/kma/commit/1e63c09568a8e7fbb7e18d470ffea5a48b60eeff

-- 
View it on GitLab: https://salsa.debian.org/med-team/kma/commit/1e63c09568a8e7fbb7e18d470ffea5a48b60eeff
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200117/d5ea90c8/attachment-0001.html>