[med-svn] [Git][med-team/kma][upstream] New upstream version 1.3.5

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / kma


Commits:
51a0802d by Nilesh Patra at 2020-10-18T11:46:38+05:30
New upstream version 1.3.5
- - - - -


4 changed files:

- kma.c
- runkma.c
- spltdb.c
- version.h


Changes:

=====================================
kma.c
=====================================
@@ -530,6 +530,7 @@ int kma_main(int argc, char *argv[]) {
 				alnToMatPtr = alnToMatDense;
 			} else if(strcmp(argv[args], "-sasm") == 0) {
 				assembly_KMA_Ptr = &skip_assemble_KMA;
+				ID_t = 0.0;
 			} else if(strcmp(argv[args], "-matrix") == 0) {
 				print_matrix = 1;
 			} else if(strcmp(argv[args], "-a") == 0) {
@@ -635,7 +636,7 @@ int kma_main(int argc, char *argv[]) {
 				if(args < argc) {
 					bcd = strtol(argv[args], &exeBasic, 10);
 					if(*exeBasic != 0) {
-						fprintf(stderr, "Invalid argument at \"-ID\".\n");
+						fprintf(stderr, "Invalid argument at \"-bcd\".\n");
 						exit(1);
 					}
 				}


=====================================
runkma.c
=====================================
@@ -2385,14 +2385,19 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
 					cover = 100.0 * aln_len / t_len;
 					q_cover = 100.0 * t_len / aln_len;
 				} else {
-					aln_len = 0;
 					id = 0;
+					q_id = 0;
+					depth = aligned_assem->depth;
+					depth /= t_len;
+					aln_len = aligned_assem->aln_len;
+					cover = 100.0 * aln_len / t_len;
+					q_cover = 0;
 				}
 				
 				if(xml) {
 					capIterXML(xml_out, DB_size, seqin_size, t_len, readCounts[template], p_value, read_score, aligned_assem->q, aln_len);
 				}
-				if(ID_t <= id && 0 < id) {
+				if(ID_t <= id) {
 					/* Output result */
 					fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
 						thread->template_name, read_score, (unsigned) expected, t_len, id, cover, q_id, q_cover, (double) depth, (double) q_value, p_value);
@@ -2427,7 +2432,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
 						depth /= t_len;
 						aln_len = aligned_assem->aln_len;
 						cover = 100.0 * aln_len / t_len;
-						q_cover = 100.0 * t_len / aln_len;
+						q_cover = 0;
 						fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
 							thread->template_name, read_score, (unsigned) expected, t_len, 0.0, cover, 0.0, q_cover, (double) depth, (double) q_value, p_value);
 						if(extendedFeatures) {


=====================================
spltdb.c
=====================================
@@ -1633,14 +1633,19 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,
 					q_cover = 100.0 * t_len / aln_len;
 				} else {
 					id = 0;
-					aln_len = 0;
+					q_id = 0;
+					depth = aligned_assem->depth;
+					depth /= t_len;
+					aln_len = aligned_assem->aln_len;
+					cover = 100.0 * aln_len / t_len;
+					q_cover = 0;
 				}
 				
 				if(xml) {
 					capIterXML(xml_out, DB_size, seqin_size, t_len, readCounts[template], p_value, read_score, aligned_assem->q, aln_len);
 				}
 				
-				if(ID_t <= id && 0 < id) {
+				if(ID_t <= id) {
 					/* Output result */
 					fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
 						thread->template_name, read_score, (unsigned) expected, t_len, id, cover, q_id, q_cover, (double) depth, (double) q_value, p_value);


=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
  * limitations under the License.
 */
 
-#define KMA_VERSION "1.3.4"
+#define KMA_VERSION "1.3.5"



View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/51a0802d7b4de7202aba09915798d7a01ebcda0b

-- 
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/51a0802d7b4de7202aba09915798d7a01ebcda0b
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