htslib/bcf_sr_sort.c at develop · SelfHacked/htslib · GitHub

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Author: Petr Danecek <pd3@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in

all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

THE SOFTWARE.

#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h

#include <config.h>

#include <assert.h>

#include <strings.h>

#include "bcf_sr_sort.h"

#include "htslib/khash_str2int.h"

#include "htslib/kbitset.h"

#define SR_REF 1

#define SR_SNP 2

#define SR_INDEL 4

#define SR_OTHER 8

#define SR_SCORE(srt,a,b) (srt)->score[((a)<<4)|(b)]

// Logical AND

static inline int kbs_logical_and(kbitset_t *bs1, kbitset_t *bs2)

{

// General case, bitsets of unequal size:

// int i, n = bs1->n < bs2->n ? bs1->n : bs2->n;

int i, n = bs1->n;

for (i=0; i<n; i++) if ( bs1->b[i] & bs2->b[i] ) return 1;

return 0;

}

// Bitwise OR, dst will be modified, src will be left unchanged

static inline void kbs_bitwise_or(kbitset_t *dst, kbitset_t *src)

{

int i;

for (i=0; i<dst->n; i++) dst->b[i] |= src->b[i];

}

static void bcf_sr_init_scores(sr_sort_t *srt)

{

int i,jbit,kbit;

// lower number = lower priority, zero means forbidden

if ( srt->pair & BCF_SR_PAIR_ANY ) srt->pair |= (BCF_SR_PAIR_SNPS | BCF_SR_PAIR_INDELS | BCF_SR_PAIR_SNP_REF | BCF_SR_PAIR_INDEL_REF);

if ( srt->pair & BCF_SR_PAIR_SNPS ) SR_SCORE(srt,SR_SNP,SR_SNP) = 3;

if ( srt->pair & BCF_SR_PAIR_INDELS ) SR_SCORE(srt,SR_INDEL,SR_INDEL) = 3;

if ( srt->pair & BCF_SR_PAIR_SNP_REF )

{

SR_SCORE(srt,SR_SNP,SR_REF) = 2;

SR_SCORE(srt,SR_REF,SR_SNP) = 2;

}

if ( srt->pair & BCF_SR_PAIR_INDEL_REF )

{

SR_SCORE(srt,SR_INDEL,SR_REF) = 2;

SR_SCORE(srt,SR_REF,SR_INDEL) = 2;

}

if ( srt->pair & BCF_SR_PAIR_ANY )

{

for (i=0; i<256; i++)

if ( !srt->score[i] ) srt->score[i] = 1;

}

// set all combinations

for (i=0; i<256; i++)

{

if ( srt->score[i] ) continue; // already set

int max = 0;

for (jbit=0; jbit<4; jbit++) // high bits

{

int j = 1<<jbit;

if ( !(i & (j<<4)) ) continue;

for (kbit=0; kbit<4; kbit++) // low bits

{

int k = 1<<kbit;

if ( !(i & k) ) continue;

if ( max < SR_SCORE(srt,j,k) ) max = SR_SCORE(srt,j,k);

}

srt->score[i] = max;

}

static int multi_is_exact(var_t *avar, var_t *bvar)

{

if ( avar->nalt != bvar->nalt ) return 0;

int alen = strlen(avar->str);

int blen = strlen(bvar->str);

if ( alen != blen ) return 0;

char *abeg = avar->str;

while ( *abeg )

{

char *aend = abeg;

while ( *aend && *aend!=',' ) aend++;

char *bbeg = bvar->str;

while ( *bbeg )

{

char *bend = bbeg;

while ( *bend && *bend!=',' ) bend++;

if ( bend - bbeg == aend - abeg && !strncasecmp(abeg,bbeg,bend-bbeg) ) break;

bbeg = *bend ? bend+1 : bend;

}

if ( !*bbeg ) return 0;

abeg = *aend ? aend+1 : aend;

}

return 1;

}

static int multi_is_subset(var_t *avar, var_t *bvar)

{

char *abeg = avar->str;

while ( *abeg )

{

char *aend = abeg;

while ( *aend && *aend!=',' ) aend++;

char *bbeg = bvar->str;

while ( *bbeg )

{

char *bend = bbeg;

while ( *bend && *bend!=',' ) bend++;

if ( bend - bbeg == aend - abeg && !strncasecmp(abeg,bbeg,bend-bbeg) ) return 1;

bbeg = *bend ? bend+1 : bend;

}

abeg = *aend ? aend+1 : aend;

}

return 0;

}

static uint32_t pairing_score(sr_sort_t *srt, int ivset, int jvset)

{

varset_t *iv = &srt->vset[ivset];

varset_t *jv = &srt->vset[jvset];

// Restrictive logic: the strictest type from a group is selected,

// so that, for example, snp+ref does not lead to the inclusion of an indel

int i,j;

uint32_t min = UINT32_MAX;

for (i=0; i<iv->nvar; i++)

{

var_t *ivar = &srt->var[iv->var[i]];

for (j=0; j<jv->nvar; j++)

{

var_t *jvar = &srt->var[jv->var[j]];

if ( srt->pair & BCF_SR_PAIR_EXACT )

{

if ( ivar->type != jvar->type ) continue;

if ( !strcmp(ivar->str,jvar->str) ) return UINT32_MAX; // exact match, best possibility

if ( multi_is_exact(ivar,jvar) ) return UINT32_MAX; // identical alleles

continue;

}

if ( ivar->type==jvar->type && !strcmp(ivar->str,jvar->str) ) return UINT32_MAX; // exact match, best possibility

if ( ivar->type & jvar->type && multi_is_subset(ivar,jvar) ) return UINT32_MAX; // one of the alleles is identical

uint32_t score = SR_SCORE(srt,ivar->type,jvar->type);

if ( !score ) return 0; // some of the varsets in the two groups are not compatible, will not pair

if ( min>score ) min = score;

}

if ( srt->pair & BCF_SR_PAIR_EXACT ) return 0;

assert( min!=UINT32_MAX );

uint32_t cnt = 0;

for (i=0; i<iv->nvar; i++) cnt += srt->var[iv->var[i]].nvcf;

for (j=0; j<jv->nvar; j++) cnt += srt->var[jv->var[j]].nvcf;

return (1u<<(28+min)) + cnt;

}

static void remove_vset(sr_sort_t *srt, int jvset)

{

if ( jvset+1 < srt->nvset )

{

varset_t tmp = srt->vset[jvset];

memmove(&srt->vset[jvset], &srt->vset[jvset+1], sizeof(varset_t)*(srt->nvset - jvset - 1));

srt->vset[srt->nvset-1] = tmp;

int *jmat = srt->pmat + jvset*srt->ngrp;

memmove(jmat, &jmat[srt->ngrp],sizeof(int)*(srt->nvset - jvset - 1)*srt->ngrp);

memmove(&srt->cnt[jvset], &srt->cnt[jvset+1], sizeof(int)*(srt->nvset - jvset - 1));

}

srt->nvset--;

}

static int merge_vsets(sr_sort_t *srt, int ivset, int jvset)

{

int i,j;

if ( ivset > jvset ) { i = ivset; ivset = jvset; jvset = i; }

varset_t *iv = &srt->vset[ivset];

varset_t *jv = &srt->vset[jvset];

kbs_bitwise_or(iv->mask,jv->mask);

i = iv->nvar;

iv->nvar += jv->nvar;

hts_expand(int, iv->nvar, iv->mvar, iv->var);

for (j=0; j<jv->nvar; j++,i++) iv->var[i] = jv->var[j];

int *imat = srt->pmat + ivset*srt->ngrp;

int *jmat = srt->pmat + jvset*srt->ngrp;

for (i=0; i<srt->ngrp; i++) imat[i] += jmat[i];

srt->cnt[ivset] += srt->cnt[jvset];

remove_vset(srt, jvset);

return ivset;

}

static int push_vset(sr_sort_t *srt, int ivset)

{

varset_t *iv = &srt->vset[ivset];

int i,j;

for (i=0; i<srt->sr->nreaders; i++)

{

vcf_buf_t *buf = &srt->vcf_buf[i];

buf->nrec++;

hts_expand(bcf1_t*,buf->nrec,buf->mrec,buf->rec);

buf->rec[buf->nrec-1] = NULL;

}

for (i=0; i<iv->nvar; i++)

{

var_t *var = &srt->var[ iv->var[i] ];

for (j=0; j<var->nvcf; j++)

{

int jvcf = var->vcf[j];

vcf_buf_t *buf = &srt->vcf_buf[jvcf];

buf->rec[buf->nrec-1] = var->rec[j];

}

remove_vset(srt, ivset);

return 0; // FIXME: check for errs in this function

}

static int cmpstringp(const void *p1, const void *p2)

{

return strcmp(* (char * const *) p1, * (char * const *) p2);

}

#if DEBUG_VSETS

void debug_vsets(sr_sort_t *srt)

{

int i,j,k;

for (i=0; i<srt->nvset; i++)

{

fprintf(stderr,"dbg_vset %d:", i);

for (j=0; j<srt->vset[i].mask->n; j++) fprintf(stderr,"%c%lu",j==0?' ':':',srt->vset[i].mask->b[j]);

fprintf(stderr,"\t");

for (j=0; j<srt->vset[i].nvar; j++)

{

var_t *var = &srt->var[srt->vset[i].var[j]];

fprintf(stderr,"\t%s",var->str);

for (k=0; k<var->nvcf; k++)

fprintf(stderr,"%c%d", k==0?':':',',var->vcf[k]);

}

fprintf(stderr,"\n");

}

#endif

#if DEBUG_VBUF

void debug_vbuf(sr_sort_t *srt)

{

int i, j;

for (j=0; j<srt->vcf_buf[0].nrec; j++)

{

fprintf(stderr,"dbg_vbuf %d:\t", j);

for (i=0; i<srt->sr->nreaders; i++)

{

vcf_buf_t *buf = &srt->vcf_buf[i];

fprintf(stderr,"\t%"PRIhts_pos, buf->rec[j] ? buf->rec[j]->pos+1 : 0);

}

fprintf(stderr,"\n");

}

#endif

static char *grp_create_key(sr_sort_t *srt)

{

if ( !srt->str.l ) return strdup("");

int i;

hts_expand(char*,srt->noff,srt->mcharp,srt->charp);

for (i=0; i<srt->noff; i++)

{

srt->charp[i] = srt->str.s + srt->off[i];

if ( i>0 ) srt->charp[i][-1] = 0;

}

qsort(srt->charp, srt->noff, sizeof(*srt->charp), cmpstringp);

char *ret = (char*) malloc(srt->str.l + 1), *ptr = ret;

for (i=0; i<srt->noff; i++)

{

int len = strlen(srt->charp[i]);

memcpy(ptr, srt->charp[i], len);

ptr += len + 1;

ptr[-1] = i+1==srt->noff ? 0 : ';';

}

return ret;

}

int bcf_sr_sort_set_active(sr_sort_t *srt, int idx)

{

hts_expand(int,idx+1,srt->mactive,srt->active);

srt->nactive = 1;

srt->active[srt->nactive - 1] = idx;

return 0; // FIXME: check for errs in this function

}

int bcf_sr_sort_add_active(sr_sort_t *srt, int idx)

{

hts_expand(int,idx+1,srt->mactive,srt->active);

srt->nactive++;

srt->active[srt->nactive - 1] = idx;

return 0; // FIXME: check for errs in this function

}

static int bcf_sr_sort_set(bcf_srs_t *readers, sr_sort_t *srt, const char *chr, hts_pos_t min_pos)

{

if ( !srt->grp_str2int )

{

// first time here, initialize

if ( !srt->pair )

{

if ( readers->collapse==COLLAPSE_NONE ) readers->collapse = BCF_SR_PAIR_EXACT;

bcf_sr_set_opt(readers, BCF_SR_PAIR_LOGIC, readers->collapse);

}

bcf_sr_init_scores(srt);

srt->grp_str2int = khash_str2int_init();

srt->var_str2int = khash_str2int_init();

}

int k;

khash_t(str2int) *hash;

hash = srt->grp_str2int;

for (k=0; k < kh_end(hash); k++)

if ( kh_exist(hash,k) ) free((char*)kh_key(hash,k));

hash = srt->var_str2int;

for (k=0; k < kh_end(hash); k++)

if ( kh_exist(hash,k) ) free((char*)kh_key(hash,k));

kh_clear(str2int, srt->grp_str2int);

kh_clear(str2int, srt->var_str2int);

srt->ngrp = srt->nvar = srt->nvset = 0;

grp_t grp;

memset(&grp,0,sizeof(grp_t));

// group VCFs into groups, each with a unique combination of variants in the duplicate lines

int ireader,ivar,irec,igrp,ivset,iact;

for (ireader=0; ireader<readers->nreaders; ireader++) srt->vcf_buf[ireader].nrec = 0;

for (iact=0; iact<srt->nactive; iact++)

{

ireader = srt->active[iact];

bcf_sr_t *reader = &readers->readers[ireader];

int rid = bcf_hdr_name2id(reader->header, chr);

grp.nvar = 0;

hts_expand(int,reader->nbuffer,srt->moff,srt->off);

srt->noff = 0;

srt->str.l = 0;

for (irec=1; irec<=reader->nbuffer; irec++)

{

bcf1_t *line = reader->buffer[irec];

if ( line->rid!=rid || line->pos!=min_pos ) break;

if ( srt->str.l ) kputc(';',&srt->str);

srt->off[srt->noff++] = srt->str.l;

size_t beg = srt->str.l;

for (ivar=1; ivar<line->n_allele; ivar++)

{

if ( ivar>1 ) kputc(',',&srt->str);

kputs(line->d.allele[0],&srt->str);

kputc('>',&srt->str);

kputs(line->d.allele[ivar],&srt->str);

}

if ( line->n_allele==1 )

{

kputs(line->d.allele[0],&srt->str);

kputsn(">.",2,&srt->str);

}

// Create new variant or attach to existing one. But careful, there can be duplicate

// records with the same POS,REF,ALT (e.g. in dbSNP-b142)

char *var_str = beg + srt->str.s;

int ret, var_idx = 0, var_end = srt->str.l;

while ( 1 )

{

ret = khash_str2int_get(srt->var_str2int, var_str, &ivar);

if ( ret==-1 ) break;

var_t *var = &srt->var[ivar];

if ( var->vcf[var->nvcf-1] != ireader ) break;

srt->str.l = var_end;

kputw(var_idx, &srt->str);

var_str = beg + srt->str.s;

var_idx++;

}

if ( ret==-1 )

{

ivar = srt->nvar++;

hts_expand0(var_t,srt->nvar,srt->mvar,srt->var);

srt->var[ivar].nvcf = 0;

khash_str2int_set(srt->var_str2int, strdup(var_str), ivar);

free(srt->var[ivar].str); // possible left-over from the previous position

}

var_t *var = &srt->var[ivar];

var->nalt = line->n_allele - 1;

var->type = bcf_get_variant_types(line);

srt->str.s[var_end] = 0;

if ( ret==-1 )

var->str = strdup(var_str);

int mvcf = var->mvcf;

var->nvcf++;

hts_expand0(int*, var->nvcf, var->mvcf, var->vcf);

if ( mvcf != var->mvcf ) var->rec = (bcf1_t **) realloc(var->rec,sizeof(bcf1_t*)*var->mvcf);

var->vcf[var->nvcf-1] = ireader;

var->rec[var->nvcf-1] = line;

grp.nvar++;

hts_expand(var_t,grp.nvar,grp.mvar,grp.var);

grp.var[grp.nvar-1] = ivar;

}

char *grp_key = grp_create_key(srt);

int ret = khash_str2int_get(srt->grp_str2int, grp_key, &igrp);

if ( ret==-1 )

{

igrp = srt->ngrp++;

hts_expand0(grp_t, srt->ngrp, srt->mgrp, srt->grp);

free(srt->grp[igrp].var);

srt->grp[igrp] = grp;

srt->grp[igrp].key = grp_key;

khash_str2int_set(srt->grp_str2int, grp_key, igrp);

memset(&grp,0,sizeof(grp_t));

}

else

free(grp_key);

srt->grp[igrp].nvcf++;

}

free(grp.var);

// initialize bitmask - which groups is the variant present in

for (ivar=0; ivar<srt->nvar; ivar++)

{

if ( kbs_resize(&srt->var[ivar].mask, srt->ngrp) < 0 )

{

fprintf(stderr, "[%s:%d %s] kbs_resize failed\n", __FILE__,__LINE__,__func__);

exit(1);

}

kbs_clear(srt->var[ivar].mask);

}

for (igrp=0; igrp<srt->ngrp; igrp++)

{

for (ivar=0; ivar<srt->grp[igrp].nvar; ivar++)

{

int i = srt->grp[igrp].var[ivar];

kbs_insert(srt->var[i].mask, igrp);

}

// create the initial list of variant sets

for (ivar=0; ivar<srt->nvar; ivar++)

{

ivset = srt->nvset++;

hts_expand0(varset_t, srt->nvset, srt->mvset, srt->vset);

varset_t *vset = &srt->vset[ivset];

vset->nvar = 1;

hts_expand0(var_t, vset->nvar, vset->mvar, vset->var);

vset->var[vset->nvar-1] = ivar;

var_t *var = &srt->var[ivar];

vset->cnt = var->nvcf;

if ( kbs_resize(&vset->mask, srt->ngrp) < 0 )

{

fprintf(stderr, "[%s:%d %s] kbs_resize failed\n", __FILE__,__LINE__,__func__);

exit(1);

}

kbs_clear(vset->mask);

kbs_bitwise_or(vset->mask, var->mask);

int type = 0;

if ( var->type==VCF_REF ) type |= SR_REF;

else

{

if ( var->type & VCF_SNP ) type |= SR_SNP;

if ( var->type & VCF_MNP ) type |= SR_SNP;

if ( var->type & VCF_INDEL ) type |= SR_INDEL;

if ( var->type & VCF_OTHER ) type |= SR_OTHER;

}

var->type = type;

}

#if DEBUG_VSETS

debug_vsets(srt);

#endif

// initialize the pairing matrix

hts_expand(int, srt->ngrp*srt->nvset, srt->mpmat, srt->pmat);

hts_expand(int, srt->nvset, srt->mcnt, srt->cnt);

memset(srt->pmat, 0, sizeof(*srt->pmat)*srt->ngrp*srt->nvset);

for (ivset=0; ivset<srt->nvset; ivset++)

{

varset_t *vset = &srt->vset[ivset];

for (igrp=0; igrp<srt->ngrp; igrp++) srt->pmat[ivset*srt->ngrp+igrp] = 0;

srt->cnt[ivset] = vset->cnt;

}

// pair the lines

while ( srt->nvset )

{

#if DEBUG_VSETS

fprintf(stderr,"\n");

debug_vsets(srt);

#endif

int imax = 0;

for (ivset=1; ivset<srt->nvset; ivset++)

if ( srt->cnt[imax] < srt->cnt[ivset] ) imax = ivset;

int ipair = -1;

uint32_t max_score = 0;

for (ivset=0; ivset<srt->nvset; ivset++)

{

if ( kbs_logical_and(srt->vset[imax].mask,srt->vset[ivset].mask) ) continue; // cannot be merged

uint32_t score = pairing_score(srt, imax, ivset);

// fprintf(stderr,"score: %d %d, logic=%d \t..\t %u\n", imax,ivset,srt->pair,score);

if ( max_score < score ) { max_score = score; ipair = ivset; }

}

// merge rows creating a new variant set this way

if ( ipair!=-1 && ipair!=imax )

{

imax = merge_vsets(srt, imax, ipair);

continue;

}

push_vset(srt, imax);

}

srt->chr = chr;

srt->pos = min_pos;

return 0; // FIXME: check for errs in this function

}

int bcf_sr_sort_next(bcf_srs_t *readers, sr_sort_t *srt, const char *chr, hts_pos_t min_pos)

{

int i,j;

assert( srt->nactive>0 );

if ( srt->nsr != readers->nreaders )

{

srt->sr = readers;

if ( srt->nsr < readers->nreaders )

{

srt->vcf_buf = (vcf_buf_t*) realloc(srt->vcf_buf,readers->nreaders*sizeof(vcf_buf_t));

memset(srt->vcf_buf + srt->nsr, 0, sizeof(vcf_buf_t)*(readers->nreaders - srt->nsr));

if ( srt->msr < srt->nsr ) srt->msr = srt->nsr;

}

srt->nsr = readers->nreaders;

srt->chr = NULL;

}

if ( srt->nactive == 1 )

{

if ( readers->nreaders>1 )

memset(readers->has_line, 0, readers->nreaders*sizeof(*readers->has_line));

bcf_sr_t *reader = &readers->readers[srt->active[0]];

assert( reader->buffer[1]->pos==min_pos );

bcf1_t *tmp = reader->buffer[0];

for (j=1; j<=reader->nbuffer; j++) reader->buffer[j-1] = reader->buffer[j];

reader->buffer[ reader->nbuffer ] = tmp;

reader->nbuffer--;

readers->has_line[srt->active[0]] = 1;

return 1;

}

if ( !srt->chr || srt->pos!=min_pos || strcmp(srt->chr,chr) ) bcf_sr_sort_set(readers, srt, chr, min_pos);

if ( !srt->vcf_buf[0].nrec ) return 0;

#if DEBUG_VBUF

debug_vbuf(srt);

#endif

int nret = 0;

for (i=0; i<srt->sr->nreaders; i++)

{

vcf_buf_t *buf = &srt->vcf_buf[i];

if ( buf->rec[0] )

{

bcf_sr_t *reader = &srt->sr->readers[i];

for (j=1; j<=reader->nbuffer; j++)

if ( reader->buffer[j] == buf->rec[0] ) break;

assert( j<=reader->nbuffer );

bcf1_t *tmp = reader->buffer[0];

reader->buffer[0] = reader->buffer[j++];

for (; j<=reader->nbuffer; j++) reader->buffer[j-1] = reader->buffer[j];

reader->buffer[ reader->nbuffer ] = tmp;

reader->nbuffer--;

nret++;

srt->sr->has_line[i] = 1;

}

else

srt->sr->has_line[i] = 0;

buf->nrec--;

if ( buf->nrec > 0 )

memmove(buf->rec, &buf->rec[1], buf->nrec*sizeof(bcf1_t*));

}

return nret;

}

void bcf_sr_sort_remove_reader(bcf_srs_t *readers, sr_sort_t *srt, int i)

{

//vcf_buf is allocated only in bcf_sr_sort_next

//So, a call to bcf_sr_add_reader() followed immediately by bcf_sr_remove_reader()

//would cause the program to crash in this segment

if (srt->vcf_buf)

{

free(srt->vcf_buf[i].rec);

if ( i+1 < srt->nsr )

memmove(&srt->vcf_buf[i], &srt->vcf_buf[i+1], (srt->nsr - i - 1)*sizeof(vcf_buf_t));

memset(srt->vcf_buf + srt->nsr - 1, 0, sizeof(vcf_buf_t));

}

sr_sort_t *bcf_sr_sort_init(sr_sort_t *srt)

{

if ( !srt ) return calloc(1,sizeof(sr_sort_t));

memset(srt,0,sizeof(sr_sort_t));

return srt;

}

void bcf_sr_sort_reset(sr_sort_t *srt)

{

srt->chr = NULL;

}

void bcf_sr_sort_destroy(sr_sort_t *srt)

{

free(srt->active);

if ( srt->var_str2int ) khash_str2int_destroy_free(srt->var_str2int);

if ( srt->grp_str2int ) khash_str2int_destroy_free(srt->grp_str2int);

int i;

for (i=0; i<srt->nsr; i++) free(srt->vcf_buf[i].rec);

free(srt->vcf_buf);

for (i=0; i<srt->mvar; i++)

{

free(srt->var[i].str);

free(srt->var[i].vcf);

free(srt->var[i].rec);

kbs_destroy(srt->var[i].mask);

}

free(srt->var);

for (i=0; i<srt->mgrp; i++)

free(srt->grp[i].var);

free(srt->grp);

for (i=0; i<srt->mvset; i++)

{

kbs_destroy(srt->vset[i].mask);

free(srt->vset[i].var);

}

free(srt->vset);

free(srt->str.s);

free(srt->off);

free(srt->charp);

free(srt->cnt);

free(srt->pmat);

memset(srt,0,sizeof(*srt));

}

htslib/bcf_sr_sort.c at develop · SelfHacked/htslib · GitHub

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