[med-svn] [Git][med-team/kma][upstream] New upstream version 1.2.16
Steffen Möller
gitlab at salsa.debian.org
Sat Nov 30 15:01:59 GMT 2019
Steffen Möller pushed to branch upstream at Debian Med / kma
Commits:
18e38cc7 by Steffen Moeller at 2019-11-30T15:00:12Z
New upstream version 1.2.16
- - - - -
6 changed files:
- align.c
- assembly.c
- kma.c
- main.c
- nw.c
- version.h
Changes:
=====================================
align.c
=====================================
@@ -601,6 +601,7 @@ AlnScore KMA_score(const HashMap_index *template_index, const unsigned char *qse
NWstat = NW_score(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, matrices, t_len);
} else {
NWstat = NW_band_score(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, band, matrices, t_len);
+ //NWstat = NW_score(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, matrices, t_len);
}
Stat.pos -= (NWstat.len - NWstat.gaps);
Stat.score = NWstat.score;
=====================================
assembly.c
=====================================
@@ -18,6 +18,7 @@
*/
#define _XOPEN_SOURCE 600
#include <ctype.h>
+#include <limits.h>
#include <math.h>
#include <stdlib.h>
#include <stdio.h>
@@ -167,7 +168,7 @@ unsigned char baseCaller(unsigned char bestNuc, unsigned char tNuc, int bestScor
} else {
/* Use MnNemars test to test significance of the base call */
if(significantBase(bestScore, depthUpdate - bestScore, evalue) == 0) {
- if(bestNuc == '-' && tNuc != '-') {
+ if(bestNuc == '-' && tNuc != '-' && bestScore != depthUpdate) {
bestNuc = 'n';
} else {
bestNuc = tolower(bestNuc);
@@ -213,7 +214,7 @@ unsigned char nanoCaller(unsigned char bestNuc, unsigned char tNuc, int bestScor
} else {
/* Use MC Neymars test to test significance of the base call */
if(significantBase(bestScore, depthUpdate - bestScore, evalue) == 0) {
- if(bestNuc == '-' && tNuc != '-') {
+ if(bestNuc == '-' && tNuc != '-' && bestScore != depthUpdate) {
bestBaseScore = 0;
for(j = 0; j < 5; ++j) {
if(bestBaseScore < calls->counts[j]) {
@@ -337,10 +338,7 @@ void * assemble_KMA_threaded(void *arg) {
if(matrix->size < (t_len << 1)) {
matrix->size = (t_len << 1);
free(matrix->assmb);
- matrix->assmb = malloc(matrix->size * sizeof(Assembly));
- if(!matrix->assmb) {
- ERROR();
- }
+ matrix->assmb = smalloc(matrix->size * sizeof(Assembly));
}
/* cpy template seq */
@@ -473,7 +471,9 @@ void * assemble_KMA_threaded(void *arg) {
while(i < aln_len) {
if(aligned->t[i] == 5) { // Template gap, insertion
if(t_len <= pos) {
- assembly[pos].counts[aligned->q[i]]++;
+ if(!++assembly[pos].counts[aligned->q[i]]) {
+ assembly[pos].counts[aligned->q[i]] = USHRT_MAX;
+ }
++i;
pos = assembly[pos].next;
} else {
@@ -517,8 +517,8 @@ void * assemble_KMA_threaded(void *arg) {
assembly[pos].counts[2] = 0;
assembly[pos].counts[3] = 0;
assembly[pos].counts[4] = 0;
- assembly[pos].counts[5] = myBias;
- assembly[pos].counts[aligned->q[i]]++;
+ assembly[pos].counts[5] = myBias < USHRT_MAX ? myBias : USHRT_MAX;
+ assembly[pos].counts[aligned->q[i]] = 1;
++i;
}
@@ -528,7 +528,9 @@ void * assemble_KMA_threaded(void *arg) {
assembly[pos].counts[5]++;
pos = assembly[pos].next;
} else {
- assembly[pos].counts[aligned->q[i]]++;
+ if(!++assembly[pos].counts[aligned->q[i]]) {
+ assembly[pos].counts[aligned->q[i]] = USHRT_MAX;
+ }
++i;
pos = assembly[pos].next;
}
@@ -651,10 +653,10 @@ void * assemble_KMA_threaded(void *arg) {
}
/* call query */
- bestNuc = 5;
- bestScore = 0;
- depthUpdate = 0;
- for(j = 0; j < 6; ++j) {
+ bestNuc = 0;
+ bestScore = assembly[pos].counts[0];
+ depthUpdate = bestScore;
+ for(j = 1; j < 6; ++j) {
if(bestScore < assembly[pos].counts[j]) {
bestScore = assembly[pos].counts[j];
bestNuc = j;
@@ -666,9 +668,9 @@ void * assemble_KMA_threaded(void *arg) {
/* check for minor base call */
if((bestScore << 1) < depthUpdate) {
if(bestNuc == '-') {
- bestBaseScore = 0;
+ bestBaseScore = assembly[pos].counts[4];
bestNuc = 4;
- for(j = 0; j < 5; ++j) {
+ for(j = 0; j < 4; ++j) {
if(bestBaseScore < assembly[pos].counts[j]) {
bestBaseScore = assembly[pos].counts[j];
bestNuc = j;
@@ -948,7 +950,9 @@ void * assemble_KMA_dense_threaded(void *arg) {
/* diff */
for(i = 0, pos = start; i < aln_len; ++i) {
if(aligned->t[i] == aligned_assem->t[pos]) {
- assembly[pos].counts[aligned->q[i]]++;
+ if(!++assembly[pos].counts[aligned->q[i]]) {
+ assembly[pos].counts[aligned->q[i]] = USHRT_MAX;
+ }
pos = assembly[pos].next;
}
}
=====================================
kma.c
=====================================
@@ -164,6 +164,7 @@ static void helpMessage(int exeStatus) {
fprintf(helpOut, "#\t-transversion\tPenalty for transversion\t-2\n");
fprintf(helpOut, "#\t-cge\t\tSet CGE penalties and rewards\tFalse\n");
fprintf(helpOut, "#\t-t\t\tNumber of threads\t\t1\n");
+ fprintf(helpOut, "#\t-c\t\tCitation\n");
fprintf(helpOut, "#\t-v\t\tVersion\n");
fprintf(helpOut, "#\t-h\t\tShows this help message\n");
fprintf(helpOut, "#\n");
@@ -789,6 +790,9 @@ int kma_main(int argc, char *argv[]) {
} else if(strcmp(argv[args], "-v") == 0) {
fprintf(stdout, "KMA-%s\n", KMA_VERSION);
exit(0);
+ } else if(strcmp(argv[args], "-c") == 0) {
+ fprintf(stdout, "Philip T.L.C. Clausen, Frank M. Aarestrup & Ole Lund, \"Rapid and precise alignment of raw reads against redundant databases with KMA\", BMC Bioinformatics, 2018;19:307.\n");
+ exit(0);
} else if(strcmp(argv[args], "-h") == 0) {
helpMessage(0);
} else {
=====================================
main.c
=====================================
@@ -24,14 +24,18 @@
#include "seq2fasta.h"
#include "update.h"
-static int helpmessage() {
+static int helpmessage(FILE *out) {
- fprintf(stderr, "# For help please use:\n");
- fprintf(stderr, "#\tkma -h\n");
- fprintf(stderr, "#\tkma index -h\n");
- fprintf(stderr, "#\tkma shm -h\n");
- fprintf(stderr, "#\tkma seq2fasta -h\n");
- fprintf(stderr, "#\tkma update -h\n");
+ fprintf(out, "# KMA enables alignment towards databases, using two k-mer mapping steps and one alignment step.\n");
+ fprintf(out, "# %16s\t%-32s\n", "Options are:", "Desc:");
+ fprintf(out, "# %16s\t%-32s\n", "", "Alignment and mapping");
+ fprintf(out, "# %16s\t%-32s\n", "index", "Indexing of databases");
+ fprintf(out, "# %16s\t%-32s\n", "shm", "Shared memory");
+ fprintf(out, "# %16s\t%-32s\n", "seq2fasta", "Conversion of database to fasta");
+ fprintf(out, "# %16s\t%-32s\n", "update", "Update database to current version");
+ fprintf(out, "# %16s\t%-32s\n", "-c", "Citation");
+ fprintf(out, "# %16s\t%-32s\n", "-v", "Version");
+ fprintf(out, "# %16s\t%-32s\n", "-h", "Help on alignment and mapping");
return 1;
}
@@ -52,11 +56,10 @@ int main(int argc, char *argv[]) {
status = update_main(argc, argv);
} else {
fprintf(stderr, "Invalid option:\t%s\n", *argv);
- status = helpmessage();
+ status = helpmessage(stderr);
}
} else {
- fprintf(stderr, "Too few arguments handed\n");
- status = helpmessage();
+ status = helpmessage(stdout);
}
return status;
=====================================
nw.c
=====================================
@@ -556,7 +556,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i
Stat.score = D_prev[n];
pos[0] = 0;
pos[1] = n;
- q_pos = n;
+ q_pos = n - en;
}
}
}
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.2.15"
+#define KMA_VERSION "1.2.16"
View it on GitLab: https://salsa.debian.org/med-team/kma/commit/18e38cc75163339bc44ef228180b9b1f62a3bee1
--
View it on GitLab: https://salsa.debian.org/med-team/kma/commit/18e38cc75163339bc44ef228180b9b1f62a3bee1
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