Nilesh Patra pushed to branch upstream at Debian Med / kma
Commits:
7da40693 by Nilesh Patra at 2022-06-26T00:50:45+05:30
New upstream version 1.4.3
- - - - -
4 changed files:
- alnfrags.c
- kma.c
- tsv.c
- version.h
Changes:
=====================================
alnfrags.c
=====================================
@@ -1151,7 +1151,7 @@ int alnFragsSE(HashMapCCI **templates_index, int
*matched_templates, int *templa
if(end == t_len) {
read_score += Wl;
}
- score = aln_len;//q_len < t_len ? q_len : t_len;
+ score = q_len < t_len ? q_len : t_len;
}
//read_score += (((start != 0) + (end !=
template_lengths[abs(template)])) * Wl);
=====================================
kma.c
=====================================
@@ -1116,8 +1116,10 @@ int kma_main(int argc, char *argv[]) {
/* -mrc 0.1 */
mrc = 0.1;
/* -apm p */
+ /*
alnFragsPE = &alnFragsPenaltyPE;
save_kmers_pair = &save_kmers_penaltyPair;
+ */
/* -lc */
kmerAnkerScore = &ankerScoreLen;
testExtension = &testExtensionScoreLen;
=====================================
tsv.c
=====================================
@@ -25,6 +25,9 @@
void initsv(FILE *outfile, long unsigned flag) {
+ /* mask off invalid flags */
+ flag &= 65535;
+
printsvField(flag, outfile, "%s%c", "Template_Name");
printsvField(flag, outfile, "%s%c", "Template_Length");
printsvField(flag, outfile, "%s%c", "Template_Identity");
@@ -47,6 +50,9 @@ void printsv(FILE *outfile, long unsigned flag, char
*template_name, Assem *alig
//printsv(tsv_out, tsv, template_name, aligned_assem, t_len, readCount,
read_score, expected, q_value, p_value, alignment_scores[template]);
+ /* mask off invalid flags */
+ flag &= 65535;
+
/* 0 no file */
if(!flag) {
return;
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.4.2"
+#define KMA_VERSION "1.4.3"
View it on GitLab:
https://salsa.debian.org/med-team/kma/-/commit/7da40693c0a28fd25aee61476e110db16406580e
--
View it on GitLab:
https://salsa.debian.org/med-team/kma/-/commit/7da40693c0a28fd25aee61476e110db16406580e
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