Commit 1e63c095 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 1.2.21

parent a28edffe

README.md

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@@ -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

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@@ -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

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@@ -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

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spltdb.c

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@@ -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];