Commit a28edffe authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 1.2.19

parent 18e38cc7

alnfrags.c

+28 −29
Original line number Diff line number Diff line
@@ -35,9 +35,9 @@ 
#include "threader.h"

#include "updatescores.h"



int (*alnFragsPE)(HashMap_index**, int*, int*, int, double, CompDNA*, CompDNA*, unsigned char*, unsigned char*, Qseqs*, Qseqs*, int, int*, int*, long unsigned*, long unsigned*, int*, int*, int*, int*, int*, int*, int, int, long*, long*, FILE*, AlnPoints*, NWmat*, volatile int*, volatile int*) = alnFragsUnionPE;

int (*alnFragsPE)(HashMap_index**, int*, int*, int, double, int, CompDNA*, CompDNA*, unsigned char*, unsigned char*, Qseqs*, Qseqs*, int, int*, int*, long unsigned*, long unsigned*, int*, int*, int*, int*, int*, int*, int, int, long*, long*, FILE*, AlnPoints*, NWmat*, volatile int*, volatile int*) = alnFragsUnionPE;



int alnFragsSE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int rc_flag, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, int q_len, int kmersize, Qseqs *header, int *bestTemplates, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *best_read_score, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB) {

int alnFragsSE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int minlen, int rc_flag, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, int q_len, int kmersize, Qseqs *header, int *bestTemplates, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *best_read_score, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB) {

	

	int t_i, template, read_score, bestHits, aln_len;

	int start, end, W1;
@@ -100,9 +100,10 @@ int alnFragsSE(HashMap_index **templates_index, int *matched_templates, int *tem 
		//read_score += (((start != 0) + (end != template_lengths[abs(template)])) * W1);

		

		/* Get normed score */

		if(aln_len > 0) {

		if(minlen <= aln_len) {

			score = 1.0 * read_score / aln_len;

		} else {

			read_score = 0;

			score = 0;

		}
@@ -142,7 +143,7 @@ int alnFragsSE(HashMap_index **templates_index, int *matched_templates, int *tem 
	return 1;

}



int alnFragsUnionPE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB) {

int alnFragsUnionPE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int minlen, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB) {

	

	int t_i, template, read_score;

	int compScore, bestHits, bestHits_r, aln_len, start, end, rc, W1;
@@ -198,13 +199,12 @@ int alnFragsUnionPE(HashMap_index **templates_index, int *matched_templates, int 
		alnStat = KMA_score(templates_index[template], qseq, qseq_comp->seqlen, qseq_comp, mq, scoreT, points, NWmatrices);

		

		/* get read score */

		if(0 < alnStat.score) {

		aln_len = alnStat.len;

			

		read_score = alnStat.score;

		if(minlen <= aln_len && 0 < read_score) {

			start = alnStat.pos;

			end = alnStat.pos + alnStat.len - alnStat.gaps;

			

			read_score = alnStat.score;

			if(start == 0 && end == template_lengths[abs(template)]) {

				read_score += abs(W1);

			}
@@ -227,13 +227,12 @@ int alnFragsUnionPE(HashMap_index **templates_index, int *matched_templates, int 
		

		alnStat = KMA_score(templates_index[template], qseq_r, qseq_r_comp->seqlen, qseq_r_comp, mq, scoreT, points, NWmatrices);

		/* get read score */

		if(0 < alnStat.score) {

		aln_len = alnStat.len;

			

		read_score = alnStat.score;

		if(minlen <= aln_len && 0 < read_score) {

			start = alnStat.pos;

			end = alnStat.pos + alnStat.len - alnStat.gaps;

			

			read_score = alnStat.score;

			if(start == 0 && end == template_lengths[abs(template)]) {

				read_score += abs(W1);

			}
@@ -421,7 +420,7 @@ int alnFragsUnionPE(HashMap_index **templates_index, int *matched_templates, int 
	return 3;

}



int alnFragsPenaltyPE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB) {

int alnFragsPenaltyPE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int minlen, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB) {

	

	int t_i, template, read_score;

	int compScore, bestHits, bestHits_r, aln_len, start, end, rc, W1, PE;
@@ -478,13 +477,12 @@ int alnFragsPenaltyPE(HashMap_index **templates_index, int *matched_templates, i 
		alnStat = KMA_score(templates_index[template], qseq, qseq_comp->seqlen, qseq_comp, mq, scoreT, points, NWmatrices);

		

		/* get read score */

		if(0 < alnStat.score) {

		aln_len = alnStat.len;

			

		read_score = alnStat.score;

		if(minlen <= aln_len && 0 < read_score) {

			start = alnStat.pos;

			end = alnStat.pos + alnStat.len - alnStat.gaps;

			

			read_score = alnStat.score;

			if(start == 0 && end == template_lengths[abs(template)]) {

				read_score += abs(W1);

			}
@@ -507,13 +505,12 @@ int alnFragsPenaltyPE(HashMap_index **templates_index, int *matched_templates, i 
		

		alnStat = KMA_score(templates_index[template], qseq_r, qseq_r_comp->seqlen, qseq_r_comp, mq, scoreT, points, NWmatrices);

		/* get read score */

		if(0 < alnStat.score) {

		aln_len = alnStat.len;

			

		read_score = alnStat.score;

		if(minlen <= aln_len && 0 < read_score) {

			start = alnStat.pos;

			end = alnStat.pos + alnStat.len - alnStat.gaps;

			

			read_score = alnStat.score;

			if(start == 0 && end == template_lengths[abs(template)]) {

				read_score += abs(W1);

			}
@@ -698,7 +695,7 @@ int alnFragsPenaltyPE(HashMap_index **templates_index, int *matched_templates, i 
	return 3;

}



int alnFragsForcePE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB) {

int alnFragsForcePE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int minlen, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB) {

	

	int t_i, template, read_score, bestHits, aln_len, W1;

	int start, end, rc;
@@ -751,11 +748,11 @@ int alnFragsForcePE(HashMap_index **templates_index, int *matched_templates, int 
		

		/* align qseq */

		alnStat = KMA_score(templates_index[template], qseq, qseq_comp->seqlen, qseq_comp, mq, scoreT, points, NWmatrices);

		if(0 < alnStat.score) {

		if(0 < alnStat.score && minlen <= alnStat.len) {

			alnStat_r = KMA_score(templates_index[template], qseq_r, qseq_r_comp->seqlen, qseq_r_comp, mq, scoreT, points, NWmatrices);

			

			/* get read score */

			if(0 < alnStat_r.score) {

			if(0 < alnStat_r.score && minlen <= alnStat_r.len) {

				aln_len = alnStat.len + alnStat_r.len;

				

				/* Handle negative insertsizes caused by trimming,
@@ -834,9 +831,10 @@ void * alnFrags_threaded(void * arg) { 
	

	static volatile int excludeIn[1] = {0}, excludeOut[1] = {0}, excludeDB[1] = {0};

	Aln_thread *thread = arg;

	int rc_flag, read_score, delta, index_in, seq_in, kmersize, flag, flag_r;

	int mq, sam, unmapped, best_read_score, stats[2], *matched_templates, *bestTemplates;

	int *best_start_pos, *best_end_pos, *template_lengths, *bestTemplates_r;

	int rc_flag, read_score, delta, index_in, seq_in, kmersize, minlen;

	int flag, flag_r, mq, sam, unmapped, best_read_score, stats[2];

	int *matched_templates, *bestTemplates, *bestTemplates_r;

	int *template_lengths, *best_start_pos, *best_end_pos;

	long *index_indexes, *seq_indexes;

	long unsigned *alignment_scores, *uniq_alignment_scores;

	double scoreT;
@@ -872,6 +870,7 @@ void * alnFrags_threaded(void * arg) { 
	points = thread->points;

	NWmatrices = thread->NWmatrices;

	kmersize = thread->kmersize;

	minlen = thread->minlen;

	mq = thread->mq;

	sam = thread->sam;

	scoreT = thread->scoreT;
@@ -910,9 +909,9 @@ void * alnFrags_threaded(void * arg) { 
		

		if(kmersize <= qseq->len) {

			if(read_score && kmersize <= qseq_r->len) { // PE

				unmapped = alnFragsPE(templates_index, matched_templates, template_lengths, mq, scoreT, qseq_comp, qseq_r_comp, qseq->seq, qseq_r->seq, header, header_r, kmersize, bestTemplates, bestTemplates_r, alignment_scores, uniq_alignment_scores, best_start_pos, best_end_pos, &flag, &flag_r, &best_read_score, &read_score, seq_in, index_in, seq_indexes, index_indexes, frag_out_raw, points, NWmatrices, excludeOut, excludeDB);

				unmapped = alnFragsPE(templates_index, matched_templates, template_lengths, mq, scoreT, minlen, qseq_comp, qseq_r_comp, qseq->seq, qseq_r->seq, header, header_r, kmersize, bestTemplates, bestTemplates_r, alignment_scores, uniq_alignment_scores, best_start_pos, best_end_pos, &flag, &flag_r, &best_read_score, &read_score, seq_in, index_in, seq_indexes, index_indexes, frag_out_raw, points, NWmatrices, excludeOut, excludeDB);

			} else { // SE

				unmapped = alnFragsSE(templates_index, matched_templates, template_lengths, mq, scoreT, rc_flag, qseq_comp, qseq_r_comp, qseq->seq, qseq_r->seq, qseq->len, kmersize, header, bestTemplates, alignment_scores, uniq_alignment_scores, best_start_pos, best_end_pos, &flag, &best_read_score, seq_in, index_in, seq_indexes, index_indexes, frag_out_raw, points, NWmatrices, excludeOut, excludeDB);

				unmapped = alnFragsSE(templates_index, matched_templates, template_lengths, mq, scoreT, minlen, rc_flag, qseq_comp, qseq_r_comp, qseq->seq, qseq_r->seq, qseq->len, kmersize, header, bestTemplates, alignment_scores, uniq_alignment_scores, best_start_pos, best_end_pos, &flag, &best_read_score, seq_in, index_in, seq_indexes, index_indexes, frag_out_raw, points, NWmatrices, excludeOut, excludeDB);

			}

		} else {

			unmapped = 0;

alnfrags.h

+6 −5
Original line number Diff line number Diff line
@@ -45,6 +45,7 @@ struct aln_thread { 
	int index_in;

	int seq_in;

	int kmersize;

	int minlen;

	int mq;

	int sam;

	double scoreT;
@@ -62,9 +63,9 @@ struct aln_thread { 
#define ALNTHREAD 1;

#endif



extern int (*alnFragsPE)(HashMap_index**, int*, int*, int, double, CompDNA*, CompDNA*, unsigned char*, unsigned char*, Qseqs*, Qseqs*, int, int*, int*, long unsigned*, long unsigned*, int*, int*, int*, int*, int*, int*, int, int, long*, long*, FILE*, AlnPoints*, NWmat*, volatile int*, volatile int*);

int alnFragsSE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int rc_flag, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, int q_len, int kmersize, Qseqs *header, int *bestTemplates, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *best_read_score, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB);

int alnFragsUnionPE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB);

int alnFragsPenaltyPE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB);

int alnFragsForcePE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB);

extern int (*alnFragsPE)(HashMap_index**, int*, int*, int, double, int, CompDNA*, CompDNA*, unsigned char*, unsigned char*, Qseqs*, Qseqs*, int, int*, int*, long unsigned*, long unsigned*, int*, int*, int*, int*, int*, int*, int, int, long*, long*, FILE*, AlnPoints*, NWmat*, volatile int*, volatile int*);

int alnFragsSE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int minlen, int rc_flag, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, int q_len, int kmersize, Qseqs *header, int *bestTemplates, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *best_read_score, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB);

int alnFragsUnionPE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int minlen, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB);

int alnFragsPenaltyPE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int minlen, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB);

int alnFragsForcePE(HashMap_index **templates_index, int *matched_templates, int *template_lengths, int mq, double scoreT, int minlen, CompDNA *qseq_comp, CompDNA *qseq_r_comp, unsigned char *qseq, unsigned char *qseq_r, Qseqs *header, Qseqs *header_r, int kmersize, int *bestTemplates, int *bestTemplates_r, long unsigned *alignment_scores, long unsigned *uniq_alignment_scores, int *best_start_pos, int *best_end_pos, int *flag, int *flag_r, int *best_read_score, int *best_read_score_r, int seq_in, int index_in, long *seq_indexes, long *index_indexes, FILE *frag_out_raw, AlnPoints *points, NWmat *NWmatrices, volatile int *excludeOut, volatile int *excludeDB);

void * alnFrags_threaded(void * arg);

assembly.c

+23 −5
Original line number Diff line number Diff line
@@ -279,7 +279,7 @@ void * assemble_KMA_threaded(void *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;

	int nextTemplate, file_i, file_count, delta, thread_num, mq, status, bcd;

	int stats[5], buffer[8];

	int minlen, stats[5], buffer[8];

	unsigned coverScore;

	long unsigned depth, depthVar;

	const char bases[6] = "ACGTN-";
@@ -312,6 +312,7 @@ void * assemble_KMA_threaded(void *arg) { 
	NWmatrices = thread->NWmatrices;

	delta = qseq->size;

	mq = thread->mq;

	minlen = thread->minlen;

	scoreT = thread->scoreT;

	evalue = thread->evalue;

	bcd = thread->bcd;
@@ -357,6 +358,8 @@ void * assemble_KMA_threaded(void *arg) { 
		

		/* start threads */

		aligned_assem->score = 0;

		aligned_assem->fragmentCountAln = 0;

		aligned_assem->readCountAln = 0;

		mainTemplate = template;

		thread_wait = thread_num;

		unlock(excludeMatrix);
@@ -446,9 +449,10 @@ void * assemble_KMA_threaded(void *arg) { 
						

						/* Get normed score */

						read_score = alnStat.score;

						if(0 < aln_len) {

						if(minlen <= aln_len) {

							score = 1.0 * read_score / aln_len;

						} else {

							read_score = 0;

							score = 0;

						}
@@ -463,6 +467,10 @@ void * assemble_KMA_threaded(void *arg) { 
							//lock(excludeMatrix);

							lockTime(excludeMatrix, 10)

							aligned_assem->score += read_score;

							if(!(stats[4] & 2) || (stats[4] & 64)) {

								++aligned_assem->fragmentCountAln;

							}

							++aligned_assem->readCountAln;

							

							/* diff */

							i = 0;
@@ -738,7 +746,7 @@ void * assemble_KMA_dense_threaded(void *arg) { 
	Assemble_thread *thread = arg;

	int i, j, t_len, aln_len, start, end, file_i, file_count, template, spin;

	int pos, read_score, bestScore, depthUpdate, bestBaseScore, nextTemplate;

	int sam, thread_num, mq, status, bcd, stats[5], buffer[8];

	int sam, thread_num, mq, status, bcd, minlen, stats[5], buffer[8];

	unsigned coverScore, delta;

	long unsigned depth, depthVar;

	const char bases[6] = "ACGTN-";
@@ -770,6 +778,7 @@ void * assemble_KMA_dense_threaded(void *arg) { 
	NWmatrices = thread->NWmatrices;

	delta = qseq->size;

	mq = thread->mq;

	minlen = thread->minlen;

	scoreT = thread->scoreT;

	evalue = thread->evalue;

	bcd = thread->bcd;
@@ -834,6 +843,8 @@ void * assemble_KMA_dense_threaded(void *arg) { 
		

		/* start threads */

		aligned_assem->score = 0;

		aligned_assem->fragmentCountAln = 0;

		aligned_assem->readCountAln = 0;

		mainTemplate = template;

		thread_wait = thread_num;

		unlock(excludeOut);
@@ -927,11 +938,11 @@ void * assemble_KMA_dense_threaded(void *arg) { 
						

						/* Get normed score */

						read_score = alnStat.score;

						if(0 < aln_len) {

						if(minlen <= aln_len) {

							score = 1.0 * read_score / aln_len;

						} else {

							score = 0;

							read_score = 0;

							score = 0;

						}

						

						if(0 < read_score && scoreT <= score) {
@@ -946,6 +957,10 @@ void * assemble_KMA_dense_threaded(void *arg) { 
							//lock(excludeMatrix);

							lockTime(excludeMatrix, 10)

							aligned_assem->score += read_score;

							if(!(stats[4] & 2) || (stats[4] & 64)) {

								++aligned_assem->fragmentCountAln;

							}

							++aligned_assem->readCountAln;

							

							/* diff */

							for(i = 0, pos = start; i < aln_len; ++i) {
@@ -1150,6 +1165,8 @@ void * skip_assemble_KMA(void *arg) { 
	aligned_assem->q[0] = 0;

	aligned_assem->len = t_len;

	aligned_assem->aln_len = t_len;

	aligned_assem->fragmentCountAln = 0;

	aligned_assem->readCountAln = 0;

	

	/* load reads of this template */

	file_i = 0;
@@ -1213,5 +1230,6 @@ void * skip_assemble_KMA(void *arg) { 
	

	aligned_assem->cover = 0; 

	aligned_assem->aln_len = (1 - exp((-1.0) * aligned_assem->depth / t_len)) * t_len; // expected coverage from depth

	

	return NULL;

}

assembly.h

+3 −0
Original line number Diff line number Diff line
@@ -42,6 +42,8 @@ struct assem { 
	unsigned len;

	unsigned aln_len;

	unsigned size;

	unsigned fragmentCountAln;

	unsigned readCountAln;

};



struct assembly {
@@ -62,6 +64,7 @@ struct assemble_thread { 
	int file_count;

	int spin;

	int mq;

	int minlen;

	int bcd;

	int sam;

	int thread_num;

ef.c

+5 −5
Original line number Diff line number Diff line
@@ -41,10 +41,10 @@ void initExtendedFeatures(FILE *out, char *templatefilename, unsigned totFrags, 
	strftime(Date, sizeof(Date), "%Y-%m-%d", tm);

	fprintf(out, "## date\t%s\n", Date);

	fprintf(out, "## command\t%s\n", cmd);

	fprintf(out, "# refSequence\treadCount\tfragmentCount\tmapScoreSum\trefCoveredPositions\trefConsensusSum\tbpTotal\tdepthVariance\tnucHighDepthVariance\tdepthMax\tsnpSum\tinsertSum\tdeletionSum\n");

	fprintf(out, "# refSequence\treadCount\tfragmentCount\tmapScoreSum\trefCoveredPositions\trefConsensusSum\tbpTotal\tdepthVariance\tnucHighDepthVariance\tdepthMax\tsnpSum\tinsertSum\tdeletionSum\treadCountAln\tfragmentCountAln\n");

}



void getExtendedFeatures(char *template_name, AssemInfo *matrix, long unsigned *template_seq, int t_len, Assem *aligned_assem, unsigned fragmentCount, unsigned readCount, FILE *outfile) {

void getExtendedFeatures(char *template_name, AssemInfo *matrix, long unsigned *template_seq, int t_len, Assem *aligned_assem, unsigned fragmentCount, unsigned readCount, unsigned fragmentCountAln, unsigned readCountAln, FILE *outfile) {

	

	unsigned pos, depthUpdate, maxDepth, nucHighVarSum;

	long unsigned snpSum, insertSum, deletionSum;
@@ -94,10 +94,10 @@ void getExtendedFeatures(char *template_name, AssemInfo *matrix, long unsigned * 
			}

		} while((pos = assembly[pos].next) != 0);

		

		fprintf(outfile, "%s\t%u\t%u\t%lu\t%u\t%u\t%lu\t%f\t%u\t%u\t%lu\t%lu\t%lu\n", template_name, readCount, fragmentCount, aligned_assem->score, aligned_assem->aln_len, aligned_assem->cover, aligned_assem->depth, (double) var, nucHighVarSum, maxDepth, snpSum, insertSum, deletionSum);

		fprintf(outfile, "%s\t%u\t%u\t%lu\t%u\t%u\t%lu\t%f\t%u\t%u\t%lu\t%lu\t%lu\t%u\t%u\n", template_name, readCount, fragmentCount, aligned_assem->score, aligned_assem->aln_len, aligned_assem->cover, aligned_assem->depth, (double) var, nucHighVarSum, maxDepth, snpSum, insertSum, deletionSum, readCountAln, fragmentCountAln);

	} else if(aligned_assem) {

		fprintf(outfile, "%s\t%u\t%u\t%u\t%u\t%u\t%lu\t%f\t%u\t%u\t%u\t%u\t%u\n", template_name, readCount, fragmentCount, 0, 0, 0, aligned_assem->depth, 0.0, 0, 0, 0, 0, 0);

		fprintf(outfile, "%s\t%u\t%u\t%u\t%u\t%u\t%lu\t%f\t%u\t%u\t%u\t%u\t%u\t%u\t%u\n", template_name, readCount, fragmentCount, 0, 0, 0, aligned_assem->depth, 0.0, 0, 0, 0, 0, 0, readCountAln, fragmentCountAln);

	} else {

		fprintf(outfile, "%s\t%u\t%u\t%u\t%u\t%u\t%u\t%f\t%u\t%u\t%u\t%u\t%u\n", template_name, 0, 0, 0, 0, 0, 0, 0.0, 0, 0, 0, 0, 0);

		fprintf(outfile, "%s\t%u\t%u\t%u\t%u\t%u\t%u\t%f\t%u\t%u\t%u\t%u\t%u\t%u\t%u\n", template_name, 0, 0, 0, 0, 0, 0, 0.0, 0, 0, 0, 0, 0, 0, 0);

	}

}