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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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