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

+kma (1.2.21-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+
+ -- Steffen Moeller <moeller@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;

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"