New upstream version 1.2.12 (d16e92cc) · Commits · Debian Med / kma

Makefile

+2 −1

Original line number	Diff line number	Diff line
		CFLAGS = -Wall -O3 -std=c99
		LIBS = align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o tmp.o update.o updateindex.o updatescores.o valueshash.o vcf.o
		LIBS = align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmerlink.o kmers.o kmmap.o loadupdate.o makeindex.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o tmp.o update.o updateindex.o updatescores.o valueshash.o vcf.o
		PROGS = kma kma_index kma_shm kma_update

		.c .o:
		@@ -46,6 +46,7 @@ index.o: index.h compress.h decon.h hashmap.h hashmapkma.h loadupdate.h makeinde
		kma.o: kma.h ankers.h assembly.h chain.h hashmapkma.h kmers.h mt1.h penalties.h pherror.h qseqs.h runinput.h runkma.h savekmers.h sparse.h spltdb.h tmp.h version.h
		kmapipe.o: kmapipe.h pherror.h
		kmeranker.o: kmeranker.h penalties.h
		kmerlink.o: kmerlink.h kmeranker.h
		kmers.o: kmers.h ankers.h compdna.h hashmapkma.h kmapipe.h pherror.h qseqs.h savekmers.h spltdb.h
		kmmap.o: kmmap.h hashmapkma.h
		loadupdate.o: loadupdate.h pherror.h hashmap.h hashmapkma.h updateindex.h

align.c

+7 −6

Original line number	Diff line number	Diff line
		@@ -210,7 +210,6 @@ AlnScore KMA(const HashMap_index template_index, const unsigned char qseq, int
		start = chainSeedsPtr(points, q_len, t_len, kmersize, &aligned->mapQ);
		score = points->score[start];

		//fprintf(stderr, "%d\t%d\t%d\t%d\n", t_len, mem_count, aligned->mapQ, score);
		if(aligned->mapQ < mq \|\| score < kmersize) {
		Stat.score = 0;
		Stat.len = 1;
		@@ -250,6 +249,8 @@ AlnScore KMA(const HashMap_index template_index, const unsigned char qseq, int
		NWstat = NW(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, Frag_align, matrices);
		} else {
		NWstat = NW_band(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, Frag_align, band, matrices);
		/* here */
		//NWstat = NW(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, Frag_align, matrices);
		}

		/* trim leading gaps */
		@@ -343,7 +344,7 @@ AlnScore KMA(const HashMap_index template_index, const unsigned char qseq, int
		NWstat = NW(template_index->seq, qseq, 0, t_s, t_e, q_s, q_e, Frag_align, matrices);
		} else {
		NWstat = NW_band(template_index->seq, qseq, 0, t_s, t_e, q_s, q_e, Frag_align, band, matrices);
		//NWstat = NW(template_index->seq, qseq, 0, t_s, t_e, q_s, q_e, Frag_align);
		//NWstat = NW(template_index->seq, qseq, 0, t_s, t_e, q_s, q_e, Frag_align, matrices);
		}

		memcpy(aligned->t + Stat.len, Frag_align->t, NWstat.len);
		@@ -377,7 +378,7 @@ AlnScore KMA(const HashMap_index template_index, const unsigned char qseq, int
		NWstat = NW(template_index->seq, qseq, 1 + (t_e == t_len), t_s, t_e, q_s, q_e, Frag_align, matrices);
		} else {
		NWstat = NW_band(template_index->seq, qseq, 1 + (t_e == t_len), t_s, t_e, q_s, q_e, Frag_align, band, matrices);
		//NWstat = NW(template_index->seq, qseq, 1 + (t_e == t_len), t_s, t_e, q_s, q_e, Frag_align);
		//NWstat = NW(template_index->seq, qseq, 1 + (t_e == t_len), t_s, t_e, q_s, q_e, Frag_align, matrices);
		}
		/* trim trailing gaps */
		if(t_e == t_len) {
		@@ -390,12 +391,12 @@ AlnScore KMA(const HashMap_index template_index, const unsigned char qseq, int
		--bias;
		}
		++bias;
		/*


		if(bias != NWstat.len) {
		NWstat.score -= (W1 + (NWstat.len - bias) * U);
		//NWstat.score -= (W1 + (NWstat.len - bias) * U);
		NWstat.len = bias;
		}
		*/
		}

		memcpy(aligned->t + Stat.len, Frag_align->t, NWstat.len);

assembly.c

+4 −3

Original line number	Diff line number	Diff line
		@@ -274,7 +274,6 @@ void * assemble_KMA_threaded(void *arg) {

		static volatile int excludeIn[1] = {0}, excludeOut[1] = {0}, excludeMatrix[1] = {0}, mainTemplate = -2, thread_wait = 0;
		static char *template_name;
		static HashMap_index *template_index;
		Assemble_thread *thread = arg;
		int i, j, t_len, aln_len, start, end, bias, myBias, gaps, pos, spin, sam;
		int read_score, depthUpdate, bestBaseScore, bestScore, template, asm_len;
		@@ -295,6 +294,7 @@ void * assemble_KMA_threaded(void *arg) {
		AssemInfo *matrix;
		AlnPoints *points;
		NWmat *NWmatrices;
		HashMap_index *template_index;

		/* get input */
		template = thread->template;
		@@ -317,6 +317,7 @@ void * assemble_KMA_threaded(void *arg) {
		sam = thread->sam;
		spin = thread->spin;
		thread_num = thread->thread_num;
		template_index = thread->template_index;

		if(template != -2) {
		/* all assemblies done,
		@@ -331,7 +332,6 @@ void * assemble_KMA_threaded(void *arg) {
		/* Allocate assembly arrays */
		lock(excludeMatrix);
		template_name = thread->template_name;
		template_index = thread->template_index;
		t_len = template_index->len;
		matrix->len = t_len;
		if(matrix->size < (t_len << 1)) {
		@@ -552,6 +552,7 @@ void * assemble_KMA_threaded(void *arg) {
		header->seq[header->len - 1] = 0;
		samwrite(qseq, header, 0, template_name, aligned, stats);
		}

		} else if(sam) {
		stats[1] = read_score;
		stats[2] = start;
		@@ -617,7 +618,6 @@ void * assemble_KMA_threaded(void *arg) {

		return NULL;
		}

		/* diff */
		/* pre on dense */
		/* Pepare and make alignment on consensus */
		@@ -697,6 +697,7 @@ void * assemble_KMA_threaded(void *arg) {
		pos = assembly[pos].next;
		}


		/* Trim alignment on consensus */
		coverScore = 0;
		bias = 0;

compress.c

+57 −4

Original line number	Diff line number	Diff line
		@@ -20,6 +20,7 @@
		#include <limits.h>
		#include <stdio.h>
		#include <stdlib.h>
		#include <sys/param.h>
		#include "compress.h"
		#include "hashmap.h"
		#include "hashmapkma.h"
		@@ -44,6 +45,7 @@ static void mmapinit(HashMapKMA finalDB, long unsigned size, FILE out) {
		if(finalDB->exist == MAP_FAILED) {
		ERROR();
		}
		posix_madvise(finalDB->exist, size, POSIX_MADV_SEQUENTIAL);
		*finalDB->exist++ = finalDB->DB_size;
		*finalDB->exist++ = finalDB->kmersize;
		*finalDB->exist++ = finalDB->prefix_len;
		@@ -72,8 +74,8 @@ HashMapKMA * compressKMA_DB(HashMap templates, FILE out) {
		void *data;
		long unsigned i, j, check, size, v_size;
		long unsigned index, t_index, v_index, new_index, null_index;
		unsigned swap, *values;
		short unsigned *values_s;
		unsigned swap, values, finalV;
		short unsigned values_s, finalV_s;
		HashMapKMA *finalDB;
		ValuesHash *shmValues;
		ValuesTable node, next, *table;
		@@ -227,6 +229,7 @@ HashMapKMA * compressKMA_DB(HashMap templates, FILE out) {
		if(finalDB->exist == MAP_FAILED) {
		ERROR();
		}
		posix_madvise(finalDB->exist, size, POSIX_MADV_SEQUENTIAL);
		finalDB->exist_l = (long unsigned *) (finalDB->exist + 3);
		finalDB->exist_l += 5;

		@@ -470,6 +473,17 @@ HashMapKMA * compressKMA_DB(HashMap templates, FILE out) {
		/* move values */
		if(finalDB->DB_size < USHRT_MAX) {
		for(node = table; node != 0; node = next) {
		next = node->next;
		values_s = (short unsigned *)(node->values);
		finalV_s = finalDB->values_s + node->v_index - 1;
		i = 2 + *values_s--;
		while(--i) {
		++finalV_s = ++values_s;
		}
		free(node->values);
		free(node);

		/*
		next = node->next;
		values_s = (short unsigned *)(node->values);
		for(i = node->v_index, j = 0; j <= *values_s; ++i, ++j) {
		@@ -477,9 +491,21 @@ HashMapKMA * compressKMA_DB(HashMap templates, FILE out) {
		}
		free(values_s);
		free(node);
		*/
		}
		} else {
		for(node = table; node != 0; node = next) {
		next = node->next;
		values = node->values;
		finalV = finalDB->values + node->v_index - 1;
		i = 2 + *values--;
		while(--i) {
		++finalV = ++values;
		}
		free(node->values);
		free(node);

		/*
		next = node->next;
		values = node->values;
		for(i = node->v_index, j = 0; j <= *values; ++i, ++j) {
		@@ -487,6 +513,7 @@ HashMapKMA * compressKMA_DB(HashMap templates, FILE out) {
		}
		free(values);
		free(node);
		*/
		}
		}

		@@ -537,8 +564,8 @@ HashMapKMA * compressKMA_DB(HashMap templates, FILE out) {
		HashMapKMA * compressKMA_megaDB(HashMap templates, FILE out) {

		long unsigned i, j, v_index, new_index, null_index, size, v_size;
		unsigned check, swap, *values;
		short unsigned *values_s;
		unsigned check, swap, values, finalV;
		short unsigned values_s, finalV_s;
		HashMapKMA *finalDB;
		ValuesHash *shmValues;
		ValuesTable node, next, *table;
		@@ -653,6 +680,7 @@ HashMapKMA * compressKMA_megaDB(HashMap templates, FILE out) {
		if(finalDB->exist == MAP_FAILED) {
		ERROR();
		}
		posix_madvise(finalDB->exist, size, POSIX_MADV_SEQUENTIAL);
		finalDB->exist_l = (long unsigned *) (finalDB->exist + 3);
		finalDB->exist_l += 5;
		} else {
		@@ -810,6 +838,7 @@ HashMapKMA * compressKMA_megaDB(HashMap templates, FILE out) {
		if(finalDB->values == MAP_FAILED) {
		ERROR();
		}
		posix_madvise(finalDB->values, size, POSIX_MADV_SEQUENTIAL);
		finalDB->values = ((void *) finalDB->values) + v_size;
		if(finalDB->DB_size < USHRT_MAX) {
		finalDB->values_s = (short unsigned *) finalDB->values;
		@@ -819,6 +848,17 @@ HashMapKMA * compressKMA_megaDB(HashMap templates, FILE out) {
		/* move values */
		if(finalDB->DB_size < USHRT_MAX) {
		for(node = table; node != 0; node = next) {
		next = node->next;
		values_s = (short unsigned *)(node->values);
		finalV_s = finalDB->values_s + node->v_index - 1;
		i = 2 + *values_s--;
		while(--i) {
		++finalV_s = ++values_s;
		}
		free(node->values);
		free(node);

		/*
		next = node->next;
		values_s = (short unsigned *)(node->values);
		for(i = node->v_index, j = 0; j <= *values_s; ++i, ++j) {
		@@ -826,9 +866,21 @@ HashMapKMA * compressKMA_megaDB(HashMap templates, FILE out) {
		}
		free(values_s);
		free(node);
		*/
		}
		} else {
		for(node = table; node != 0; node = next) {
		next = node->next;
		values = node->values;
		finalV = finalDB->values + node->v_index - 1;
		i = 2 + *values--;
		while(--i) {
		++finalV = ++values;
		}
		free(node->values);
		free(node);

		/*
		next = node->next;
		values = node->values;
		for(i = node->v_index, j = 0; j <= *values; ++i, ++j) {
		@@ -836,6 +888,7 @@ HashMapKMA * compressKMA_megaDB(HashMap templates, FILE out) {
		}
		free(values);
		free(node);
		*/
		}
		}
		/* dump final DB */

hashmapindex.c

+31 −10

Original line number	Diff line number	Diff line
		@@ -37,17 +37,26 @@ typedef int key_t;
		void (destroyPtr)(HashMap_index ) = &alignClean;
		HashMap_index * (alignLoadPtr)(HashMap_index , int, int, int, int, long unsigned, long unsigned) = &alignLoad_fly;

		void hashMap_index_initialize(HashMap_index *dest, int len, int kmerindex) {
		int hashMap_index_initialize(HashMap_index *dest, int len, int kmerindex) {

		dest->len = len;
		dest->size = len << 1;
		dest->kmerindex = kmerindex;

		if(dest->size < (len << 1)) {
		if(dest->size) {
		free(dest->index);
		free(dest->seq);
		}
		dest->size = len << 1;
		dest->index = calloc(dest->size, sizeof(int));
		dest->seq = malloc(((len >> 5) + 1) * sizeof(long unsigned));
		if(!dest->index \|\| !dest->seq) {
		ERROR();
		}

		return 0;
		}

		return 1;
		}

		void hashMap_index_set(HashMap_index *dest) {
		@@ -248,8 +257,13 @@ HashMap_index * hashMap_index_load(HashMap_index *src, int seq, int index, int l

		if(src == 0) {
		src = smalloc(sizeof(HashMap_index));
		src->size = 0;
		}
		if(hashMap_index_initialize(src, len, kmersize)) {
		src->size = len << 1;
		memset(src->index, 0, src->size * sizeof(int));
		}
		hashMap_index_initialize(src, len, kmersize);

		read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
		read(index, src->index, src->size * sizeof(int));

		@@ -267,8 +281,13 @@ HashMap_index * hashMap_index_build(HashMap_index *src, int seq, int len, int km

		if(src == 0) {
		src = smalloc(sizeof(HashMap_index));
		src->size = 0;
		}

		if(hashMap_index_initialize(src, len, kmersize)) {
		memset(src->index, 0, src->size * sizeof(int));
		}
		hashMap_index_initialize(src, len, kmersize);

		shifter = sizeof(long unsigned) * sizeof(long unsigned) - (src->kmerindex << 1);

		read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
		@@ -375,10 +394,12 @@ HashMap_index * alignLoad_shm_initial(char *templatefilename, int file_len, int
		}

		void alignClean(HashMap_index *template_index) {

		/* Overwrite later */
		/*
		if(template_index) {
		hashMap_index_destroy(template_index);
		}
		*/
		}

		void alignClean_shm(HashMap_index *template_index) {