[med-svn] [Git][med-team/kma][upstream] New upstream version 1.2.22

[Steffen Möller]

Steffen Möller pushed to branch upstream at Debian Med / kma


Commits:
b6cdab00 by Steffen Moeller at 2020-04-26T01:31:06+02:00
New upstream version 1.2.22
- - - - -


4 changed files:

- index.c
- makeindex.c
- makeindex.h
- version.h


Changes:

=====================================
index.c
=====================================
@@ -65,6 +65,7 @@ static void helpMessage(int exeStatus) {
 	fprintf(helpOut, "#\t-ht\t\tHomology template\t\t\t1.0\n");
 	fprintf(helpOut, "#\t-hq\t\tHomology query\t\t\t\t1.0\n");
 	fprintf(helpOut, "#\t-and\t\tBoth homolgy thresholds\n#\t\t\thas to be reached\t\t\tor\n");
+	fprintf(helpOut, "#\t-nbp\t\tNo bias print\t\t\t\tFalse\n");
 	fprintf(helpOut, "#\t-v\t\tVersion\n");
 	fprintf(helpOut, "#\t-h\t\tShows this help message\n");
 	fprintf(helpOut, "#\n");
@@ -452,6 +453,8 @@ int index_main(int argc, char *argv[]) {
 			megaDB = 1;
 		} else if(strcmp(argv[args], "-NI") == 0) {
 			dumpIndex = &dumpSeq;
+		} else if(strcmp(argv[args], "-nbp") == 0) {
+			biasPrintPtr = &biasNoPrint;
 		} else if(strcmp(argv[args], "-v") == 0) {
 			fprintf(stdout, "KMA_index-%s\n", KMA_VERSION);
 			exit(0);


=====================================
makeindex.c
=====================================
@@ -31,6 +31,16 @@
 #include "seqparse.h"
 #include "updateindex.h"
 
+int (*biasPrintPtr)(FILE*, char*, unsigned char*, int) = &biasPrint;
+
+int biasPrint(FILE *name_out, char *format, unsigned char *name, int bias) {
+	return fprintf(name_out, "%s B%d\n", name, bias);
+}
+
+int biasNoPrint(FILE *name_out, char *format, unsigned char *name, int bias) {
+	return fprintf(name_out, "%s\n", name);
+}
+
 void makeDB(HashMap *templates, int kmerindex, char **inputfiles, int fileCount, char *outputfilename, int appender, char *trans, int MinLen, int MinKlen, double homQ, double homT, unsigned **template_lengths, unsigned **template_ulengths, unsigned **template_slengths) {
 	
 	int fileCounter, file_len, bias, FASTQ;
@@ -110,7 +120,7 @@ void makeDB(HashMap *templates, int kmerindex, char **inputfiles, int fileCount,
 						*seq = 0;
 					}
 					if(bias > 0) {
-						fprintf(name_out, "%s B%d\n", header->seq + 1, bias);
+						biasPrintPtr(name_out, "%s B%d\n", header->seq + 1, bias);
 					} else {
 						fprintf(name_out, "%s\n", header->seq + 1);
 					}


=====================================
makeindex.h
=====================================
@@ -18,4 +18,7 @@
 */
 #include "hashmap.h"
 
+extern int (*biasPrintPtr)(FILE*, char*, unsigned char*, int);
+int biasPrint(FILE *name_out, char *format, unsigned char *name, int bias);
+int biasNoPrint(FILE *name_out, char *format, unsigned char *name, int bias);
 void makeDB(HashMap *templates, int kmerindex, char **inputfiles, int fileCount, char *outputfilename, int appender, char *trans, int MinLen, int MinKlen, double homQ, double homT, unsigned **template_lengths, unsigned **template_ulengths, unsigned **template_slengths);


=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
  * limitations under the License.
 */
 
-#define KMA_VERSION "1.2.21"
+#define KMA_VERSION "1.2.22"



View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/b6cdab004655ea4b7164c28fb57cbef8e5555397

-- 
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/b6cdab004655ea4b7164c28fb57cbef8e5555397
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200425/fdb902ee/attachment-0001.html>