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abcWriteBcf.cpp
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abcWriteBcf.cpp
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/*
This is a class that dumps BCF output. Its mainly a wrapper around other classes here in angsd. Maybe this should be streamlined abit
*/
#include <htslib/hts.h>
#include <htslib/vcf.h>
#include <htslib/kstring.h>
#include <htslib/kseq.h>
#include "analysisFunction.h"
#include "shared.h"
#include "abcFreq.h"
#include "abcCallGenotypes.h"
#include "abcMajorMinor.h"
#include "abcWriteBcf.h"
#include "aio.h"
#include "abcMcall.h"
#include "abcCounts.h"
void error(const char *format, ...)
{
va_list ap;
va_start(ap, format);
vfprintf(stderr, format, ap);
va_end(ap);
exit(-1);
}
void abcWriteBcf::printArg(FILE *argFile){
fprintf(argFile,"------------------------\n%s:\n",__FILE__);
fprintf(argFile,"\t-doBcf\t%d\n",doBcf);
fprintf(argFile,"\t1: (still beta, not really working)\n");
fprintf(argFile,"\n\tNB This is a wrapper around -gl -domajorminor and -dopost -dogeno\n");
}
void abcWriteBcf::run(funkyPars *pars){
if(doBcf==0)
return ;
}
//last is from abc.h
void print_bcf_header(htsFile *fp,bcf_hdr_t *hdr,argStruct *args,kstring_t &buf,const bam_hdr_t *bhdr,int domcall){
if(args->ref){
buf.l = 0;
ksprintf(&buf, "##reference=file://%s\n", args->ref);
bcf_hdr_append(hdr,buf.s);
}
if (args->anc){
buf.l = 0;
ksprintf(&buf, "##ancestral=file://%s\n", args->anc);
bcf_hdr_append(hdr,buf.s);
}
// Translate BAM @SQ tags to BCF ##contig tags
// todo: use/write new BAM header manipulation routines, fill also UR, M5
for (int i=0; i<bhdr->n_targets; i++){
buf.l = 0;
ksprintf(&buf, "##contig=<ID=%s,length=%d>", bhdr->target_name[i], bhdr->target_len[i]);
bcf_hdr_append(hdr, buf.s);
}
buf.l = 0;
bcf_hdr_append(hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
bcf_hdr_append(hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
bcf_hdr_append(hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of raw reads supporting an indel\">");
bcf_hdr_append(hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of raw reads supporting an indel\">");
bcf_hdr_append(hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
bcf_hdr_append(hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
bcf_hdr_append(hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
bcf_hdr_append(hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
bcf_hdr_append(hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
bcf_hdr_append(hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
bcf_hdr_append(hdr,"##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">");
bcf_hdr_append(hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
bcf_hdr_append(hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
bcf_hdr_append(hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
bcf_hdr_append(hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
bcf_hdr_append(hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
bcf_hdr_append(hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
bcf_hdr_append(hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
bcf_hdr_append(hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
if(domcall){
bcf_hdr_append(hdr,"##INFO=<ID=QS_angsd,Number=R,Type=Float,Description=\"Sum of quality scores for A,C,G,T,N \">");
bcf_hdr_append(hdr,"##INFO=<ID=Quals_angsd ,Number=R,Type=Float,Description=\"Quality score for alternative and null hypothesis\">");
}
bcf_hdr_append(hdr,"##INFO=<ID=AF,Number=A,Type=Float,Description=\"Minor Allele Frequency\">");
bcf_hdr_append(hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
bcf_hdr_append(hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths\">");
bcf_hdr_append(hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
bcf_hdr_append(hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=GL,Number=G,Type=Float,Description=\"scaled Genotype Likelihoods (loglikeratios to the most likely (in log10))\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype Probabilities\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=EBD,Number=4,Type=Float,Description=\"The effective basedepth\">");
//fprintf(stderr,"samples from sm:%d\n",args->sm->n);
buf.l =0;
ASSERT(args);
ksprintf(&buf, "##angsdVersion=%s",args->version);
bcf_hdr_append(hdr, buf.s);
buf.l = 0;
ksprintf(&buf, "##angsdCommand=%s;Date=%s",args->cmdline,args->datetime);
bcf_hdr_append(hdr, buf.s);
buf.l=0;
for(int i=0;i<args->sm->n;i++){
bcf_hdr_add_sample(hdr, args->sm->smpl[i]);
}
bcf_hdr_add_sample(hdr, NULL); // to update internal structures
if ( bcf_hdr_write(fp, hdr)!=0 )
fprintf(stderr,"Failed to write bcf\n");
buf.l=0;
}
void abcWriteBcf::clean(funkyPars *pars){
if(doBcf==0)
return;
}
void abcWriteBcf::print(funkyPars *pars){
aio::doAssert(bcf_hdr_nsamples(hdr)>0);
if(doBcf==0)
return;
// lh3struct *lh3 = (lh3struct*) pars->extras[5];
freqStruct *freq = (freqStruct *) pars->extras[7];
genoCalls *geno = (genoCalls *) pars->extras[11];
angsd_mcall *mcall = NULL;
if(domcall)
mcall = (angsd_mcall *) pars->extras[5];
for(int s=0;s<pars->numSites;s++) {
if(pars->keepSites[s]==0)
continue;
rec->rid = bcf_hdr_name2id(hdr,header->target_name[pars->refId]);
rec->pos = pars->posi[s];//<- maybe one index?
// bcf_update_id(hdr, rec, "rs6054257");
if(domcall>0&&mcall!=NULL){
//
char alleles[16];
int goa =0;
alleles[goa++] = intToRef[mcall->als[4*s]];
for(int i=1;i<4;i++)
if(mcall->als[4*s+i]==4)
break;
else{
alleles[goa++] = ',';
alleles[goa++] = intToRef[mcall->als[4*s+i]];
}
alleles[goa] = '\0';
// fprintf(stderr,"ALS: %s\n",alleles);
//exit(0);
// ={intToRef[pars->major[s]],',',intToRef[pars->minor[s]],'\0'};
bcf_update_alleles_str(hdr, rec, alleles);
}else{
char majmin[4]={intToRef[pars->major[s]],',',intToRef[pars->minor[s]],'\0'};
bcf_update_alleles_str(hdr, rec, majmin);
}
if(freq==NULL&&mcall==NULL)
rec->qual = 29;
// .. FILTER
int32_t tmpi = bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS");
bcf_update_filter(hdr, rec, &tmpi, 1);
// .. INFO
tmpi = pars->keepSites[s];
aio::doAssert(bcf_update_info_int32(hdr, rec, "NS", &tmpi, 1)==0);
if(mcall){
float *tmp = mcall->QS+5*s;
// for(int i=0;i<5;i++) fprintf(stderr,"qs[%d]: %f\n",i,tmp[i]);
aio::doAssert(bcf_update_info_float(hdr, rec, "QS_angsd", tmp, 5)==0);
tmp = mcall->quals+2*s;
aio::doAssert(bcf_update_info_float(hdr, rec, "Quals_angsd", tmp, 2)==0);
if(mcall->isvar[s]>0)
rec->qual = tmp[0];
else
rec->qual = tmp[1];
}
if(pars->counts){
int depth = 0;
for(int i=0; i<4*pars->nInd; i++)
depth += pars->counts[s][i];
tmpi = depth;
aio::doAssert(bcf_update_info_int32(hdr, rec, "DP", &tmpi, 1)==0);
}
if(freq){
float tmpf = freq->freq[s];
aio::doAssert(bcf_update_info_float(hdr, rec, "AF", &tmpf, 1)==0);
}
// .. FORMAT
// aio::doAssert(geno);
// fprintf(stderr,"bcf_hdr_nsamples(hdr): %d\n",bcf_hdr_nsamples(hdr));
if(geno&&mcall==NULL){
int32_t *tmpia = (int*)malloc(bcf_hdr_nsamples(hdr)*2*sizeof(int32_t));
for(int i=0; i<pars->nInd;i++){
if(geno->dat[s][i]==-1){
tmpia[2*i+0] = bcf_gt_missing;
tmpia[2*i+1] = bcf_gt_missing;
}else if(geno->dat[s][i]==0){
tmpia[2*i+0] = bcf_gt_unphased(0);
tmpia[2*i+1] = bcf_gt_unphased(0);
}else if(geno->dat[s][i]==1){
tmpia[2*i+0] = bcf_gt_unphased(0);
tmpia[2*i+1] = bcf_gt_unphased(1);
} else if(geno->dat[s][i]==2){
tmpia[2*i+0] = bcf_gt_unphased(1);
tmpia[2*i+1] = bcf_gt_unphased(1);
}
}
bcf_update_genotypes(hdr, rec, tmpia, bcf_hdr_nsamples(hdr)*2);
free(tmpia);
}
else if(mcall!=NULL){
int32_t *tmpia = (int*)malloc(bcf_hdr_nsamples(hdr)*2*sizeof(int32_t));
for(int i=0; i<pars->nInd;i++){
if(mcall->gcdat[s][2*i]==-1)
aio::doAssert(mcall->gcdat[s][2*i]==mcall->gcdat[s][2*i+1]);
if(mcall->gcdat[s][2*i]==-1){
tmpia[2*i+0] = bcf_gt_missing;
tmpia[2*i+1] = bcf_gt_missing;
}else {
tmpia[2*i+0] = bcf_gt_unphased(mcall->gcdat[s][2*i+0]);
tmpia[2*i+1] = bcf_gt_unphased(mcall->gcdat[s][2*i+1]);
}
}
bcf_update_genotypes(hdr, rec, tmpia, bcf_hdr_nsamples(hdr)*2);
free(tmpia);
}
if(pars->counts){
int32_t *tmpfa = (int32_t*)malloc(sizeof(int32_t)*bcf_hdr_nsamples(hdr));
suint *ary=pars->counts[s];
for(int i=0;i<bcf_hdr_nsamples(hdr);i++)
tmpfa[i] = ary[i*4+0]+ary[i*4+1]+ary[i*4+2]+ary[i*4+3];
bcf_update_format_int32(hdr, rec, "DP", tmpfa,bcf_hdr_nsamples(hdr) );
free(tmpfa);
}
if(pars->likes && pars->likes[s]){
float *tmpfa = (float*)malloc(3*bcf_hdr_nsamples(hdr)*sizeof(float ));
int32_t *tmpi = (int32_t*)malloc(3*bcf_hdr_nsamples(hdr)*sizeof(int32_t));
int major = pars->major[s];
int minor = pars->minor[s];
aio::doAssert(major!=4&&minor!=4);
for(int i=0;i<bcf_hdr_nsamples(hdr);i++){
double val[3];
val[0] = pars->likes[s][i*10+angsd::majorminor[major][major]];
val[1] = pars->likes[s][i*10+angsd::majorminor[major][minor]];
val[2] = pars->likes[s][i*10+angsd::majorminor[minor][minor]];
//fixed awkward case where all gls are -Inf, should only happen with -gl 6
if(std::isinf(val[0])&&std::isinf(val[1])&&std::isinf(val[2]))
val[0]=val[1]=val[2]=0;
//angsd::logrescale(val,3);
for(int j=0;j<3;j++){
tmpfa[i*3+j] = val[j]/M_LN10;
double tmptmp = -log10(exp(val[j]))*10.0;
tmpi[i*3+j] = round(tmptmp);
}
}
bcf_update_format_float(hdr, rec, "GL", tmpfa,3*bcf_hdr_nsamples(hdr) );
bcf_update_format_int32(hdr, rec, "PL", tmpi,3*bcf_hdr_nsamples(hdr) );
free(tmpfa);
free(tmpi);
}
if(pars->extras[2]){
counts *cnts = (counts*) pars->extras[2];
float *ebd = cnts->ebd[s];
bcf_update_format_float(hdr, rec, "EBD",ebd ,4*bcf_hdr_nsamples(hdr) );
}
if(pars->post&&pars->post[s]) {
float *tmpfa = (float*)malloc(3*bcf_hdr_nsamples(hdr)*sizeof(float ));
for(int i=0;i<3*bcf_hdr_nsamples(hdr);i++)
tmpfa[i] = pars->post[s][i];
for(int i=0;i<bcf_hdr_nsamples(hdr);i++)
if(tmpfa[3*i]+tmpfa[3*i+1]+tmpfa[3*i+2]==0){
bcf_float_set_missing(tmpfa[3*i]);
tmpfa[3*i+1] = tmpfa[3*i+2] = tmpfa[3*i];
}
#if 0
//this block of code was for earlier version of the vcf standard
for(int i=0;i<bcf_hdr_nsamples(hdr);i++){
double *val = pars->post[s] +i*3;
// fprintf(stderr,"va: %f %f %f\n",val[0],val[1],val[2]);
//fixed awkward case where all gls are -Inf, should only happen with -gl 6
if(std::isinf(val[0])&&std::isinf(val[1])&&std::isinf(val[2]))
val[0]=val[1]=val[2]=0;
//angsd::logrescale(val,3);
for(int j=0;j<3;j++){
tmpfa[i*3+j] = -log10(val[j])*10.0;
}
double mmax = std::min(tmpfa[i*3],std::min(tmpfa[3*i+1],tmpfa[3*i+2]));
// fprintf(stderr,"min:%f\n",mmax);
for(int j=0;j<3;j++)
tmpfa[i*3+j] -= mmax;
//angsd::logrescale(tmpfa+i*3,3);
}
#endif
bcf_update_format_float(hdr, rec, "GP", tmpfa,3*bcf_hdr_nsamples(hdr) );
free(tmpfa);
}
if ( bcf_write1(fp, hdr, rec)!=0 ){
fprintf(stderr,"Failed to write %s:%d\n",__FILE__,__LINE__);
exit(0);
}
// fprintf(stderr,"------\n");
bcf_clear1(rec);
}
}
void abcWriteBcf::getOptions(argStruct *arguments){
doBcf=angsd::getArg("-doBcf",doBcf,arguments);
if(doBcf==0)
return;
else{
fprintf(stderr,"\n[bcfoutput] \tPlease add the following parameters \n\t\t '-gl 1 -dopost 1 -domajorminor 1 -domaf 1 -dobcf 1 --ignore-RG 0 -dogeno 1 -docounts 1'\n\n");
}
refName = ancName = NULL;
gl = doMajorMinor = doCounts = doMaf = doPost = doGeno = 0;
ancName = angsd::getArg("-anc",ancName,arguments);
refName = angsd::getArg("-ref",refName,arguments);
doPost=angsd::getArg("-doPost",doPost,arguments);
doMajorMinor=angsd::getArg("-doMajorMinor",doMajorMinor,arguments);
gl=angsd::getArg("-gl",gl,arguments);
doMaf = angsd::getArg("-doMaf",doMaf,arguments);
doCounts = angsd::getArg("-doCounts",doCounts,arguments);
doGeno = angsd::getArg("-doGeno",doGeno,arguments);
domcall = angsd::getArg("-doMcall",domcall,arguments);
if(doPost==0||doMajorMinor==0||gl==0){
fprintf(stderr,"\nPotential problem. -doBcf is a wrapper around -doMajorMinor -doPost and -gl. These values must therefore be set\n\n");
// exit(0);
}
}
extern bcf_hdr_t *vcfreader_hs_bcf_hdr;
//constructor
abcWriteBcf::abcWriteBcf(const char *outfiles_a,argStruct *arguments,int inputtype) {
rec=NULL;
hdr=NULL;
fp=NULL;
doBcf =0;
args=arguments;
outfiles=outfiles_a;
domcall = 0;
if(arguments->argc==2){
if(!strcasecmp(arguments->argv[1],"-doBcf")){
printArg(stdout);
exit(0);
}else
return;
}
getOptions(arguments);
if(doBcf==0){
shouldRun[index] =0;
return;
}else
shouldRun[index] =1;
printArg(arguments->argumentFile);
kstring_t buf;
buf.s=NULL;
buf.l=buf.m=0;
fp=aio::openFileHtsBcf(outfiles,".bcf");
rec = bcf_init1();
whatIsTheInput(arguments->inputtype);
if(arguments->inputtype==INPUT_BAM||arguments->inputtype==INPUT_GLF||arguments->inputtype==INPUT_GLF3||arguments->inputtype==INPUT_GLF10_TEXT){
hdr = bcf_hdr_init("w");
print_bcf_header(fp,hdr,args,buf,header,domcall);
} else if(arguments->inputtype==INPUT_VCF_GP||arguments->inputtype==INPUT_VCF_GL){
fprintf(stderr,"\t-> Building bcf header\n");
hdr = bcf_hdr_dup(vcfreader_hs_bcf_hdr);
bcf_hdr_append(hdr,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=GL,Number=G,Type=Float,Description=\"scaled Genotype Likelihoods (loglikeratios to the most likely (in log10))\">");
bcf_hdr_append(hdr,"##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype Probabilities\">");
bcf_hdr_append(hdr,"##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">");
if(doMaf)
bcf_hdr_append(hdr,"##INFO=<ID=AF,Number=A,Type=Float,Description=\"Minor Allele Frequency\">");
ksprintf(&buf, "##angsdVersion=%s",args->version);
bcf_hdr_append(hdr, buf.s);
buf.l = 0;
ksprintf(&buf, "##angsdCommand=%s;Date=%s",args->cmdline,args->datetime);
bcf_hdr_append(hdr, buf.s);
buf.l=0;
if ( bcf_hdr_write(fp, hdr)!=0 )
fprintf(stderr,"Failed to write bcf %s:%d\n",__FILE__,__LINE__);
if(buf.s)
free(buf.s);
}
}
abcWriteBcf::~abcWriteBcf(){
if(rec)
bcf_destroy(rec);
if(hdr)
bcf_hdr_destroy(hdr);
if(fp!=NULL) hts_close(fp);
}