[med-svn] [Git][med-team/kma][master] 4 commits: New upstream version 1.2.21

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / kma


Commits:
1e63c095 by Steffen Moeller at 2020-01-17T23:29:15+01:00
New upstream version 1.2.21
- - - - -
78b0a1df by Steffen Moeller at 2020-01-17T23:29:15+01:00
routine-update: New upstream version

- - - - -
c76ad345 by Steffen Moeller at 2020-01-17T23:29:16+01:00
Update upstream source from tag 'upstream/1.2.21'

Update to upstream version '1.2.21'
with Debian dir 9c4d3149d989f4c73f68ff7aa6e189dd839f7add
- - - - -
c12c030e by Steffen Moeller at 2020-01-17T23:29:33+01:00
routine-update: Ready to upload to unstable

- - - - -


7 changed files:

- README.md
- debian/changelog
- 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:
 
 ```


=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+kma (1.2.21-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+
+ -- Steffen Moeller <moeller at debian.org>  Fri, 17 Jan 2020 23:29:19 +0100
+
 kma (1.2.19-1) unstable; urgency=medium
 
   * Team upload.


=====================================
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/compare/8e34dd7cd271ba9e5268983e3d6fd67672666176...c12c030ebcbbc41385af2247133ad4e276a0c85d

-- 
View it on GitLab: https://salsa.debian.org/med-team/kma/compare/8e34dd7cd271ba9e5268983e3d6fd67672666176...c12c030ebcbbc41385af2247133ad4e276a0c85d
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