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
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