Commit 18e38cc7 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 1.2.16

parent 3a59834b

align.c

+1 −0
Original line number Diff line number Diff line
@@ -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

+21 −17
Original line number Diff line number Diff line
@@ -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

+4 −0
Original line number Diff line number Diff line
@@ -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

+13 −10
Original line number Diff line number Diff line
@@ -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

+1 −1
Original line number Diff line number Diff line
@@ -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;

			}

		}

	}