[med-svn] [Git][med-team/kma][master] 7 commits: New upstream version 1.2.22
Steffen Möller
gitlab at salsa.debian.org
Sun Apr 26 00:36:57 BST 2020
Steffen Möller pushed to branch master at Debian Med / kma
Commits:
b6cdab00 by Steffen Moeller at 2020-04-26T01:31:06+02:00
New upstream version 1.2.22
- - - - -
bc5b0a9c by Steffen Moeller at 2020-04-26T01:31:06+02:00
routine-update: New upstream version
- - - - -
7b77da5a by Steffen Moeller at 2020-04-26T01:31:07+02:00
Update upstream source from tag 'upstream/1.2.22'
Update to upstream version '1.2.22'
with Debian dir b38af6f32b15a23e73bfeab6981d4a8128082a54
- - - - -
a3336e3d by Steffen Moeller at 2020-04-26T01:31:07+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
dd891916 by Steffen Moeller at 2020-04-26T01:31:09+02:00
routine-update: Add salsa-ci file
- - - - -
6ff4c486 by Steffen Moeller at 2020-04-26T01:31:09+02:00
routine-update: Rules-Requires-Root: no
- - - - -
f44eda4b by Steffen Moeller at 2020-04-26T01:33:39+02:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- + debian/salsa-ci.yml
- debian/upstream/metadata
- index.c
- makeindex.c
- makeindex.h
- version.h
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+kma (1.2.22-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * d/u/metadata: yamllint clean
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 26 Apr 2020 01:31:11 +0200
+
kma (1.2.21-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -5,10 +5,11 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
zlib1g-dev
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/kma
Vcs-Git: https://salsa.debian.org/med-team/kam.git
Homepage: https://bitbucket.org/genomicepidemiology/kma
+Rules-Requires-Root: no
Package: kma
Architecture: any
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,21 +1,22 @@
Reference:
- Author: Philip T. L. C. Clausen and Frank M. Aarestrup and Ole Lund
- Title: >
+ - Author: Philip T. L. C. Clausen and Frank M. Aarestrup and Ole Lund
+ Title: >
Rapid and precise alignment of raw reads against redundant databases
with KMA
- Journal: BMC Bioinformatics
- Year: 2018
- Volume: 19
- Pages: 307
- DOI: 10.1186/s12859-018-2336-6
- PMID: 30157759
- URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116485/
- eprint: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116485/pdf/12859_2018_Article_2336.pdf"
+ Journal: BMC Bioinformatics
+ Year: 2018
+ Volume: 19
+ Pages: 307
+ DOI: 10.1186/s12859-018-2336-6
+ PMID: 30157759
+ URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116485/
+ eprint: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116485/pdf/\
+ 12859_2018_Article_2336.pdf"
Registry:
-- Name: OMICtools
- Entry: OMICS_31606
-- Name: bio.tools
- Entry: NA
-- Name: conda:bioconda
- Entry: kma
+ - Name: OMICtools
+ Entry: OMICS_31606
+ - Name: bio.tools
+ Entry: NA
+ - Name: conda:bioconda
+ Entry: kma
Repository: https://bitbucket.org/genomicepidemiology/kma
=====================================
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/-/compare/c12c030ebcbbc41385af2247133ad4e276a0c85d...f44eda4b5630dc4372e3dacaf19e43af6c02b0db
--
View it on GitLab: https://salsa.debian.org/med-team/kma/-/compare/c12c030ebcbbc41385af2247133ad4e276a0c85d...f44eda4b5630dc4372e3dacaf19e43af6c02b0db
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