//read program parameters
void setArgsBam(argStruct *arguments){
int seed=0;
remove_bads = angsd::getArg("-remove_bads",remove_bads,arguments);
uniqueOnly = angsd::getArg("-uniqueOnly",uniqueOnly,arguments);
only_proper_pairs =angsd::getArg("-only_proper_pairs",only_proper_pairs,arguments);
fai_fname =angsd::getArg("-f",fai_fname,arguments);
minMapQ = angsd::getArg("-minMapQ",minMapQ,arguments);
cigstat = angsd::getArg("-cigstat",cigstat,arguments);
minQ = angsd::getArg("-minQ",minQ,arguments);
downSample = angsd::getArg("-downSample",downSample,arguments);
seed = angsd::getArg("-seed",seed,arguments);
trim = angsd::getArg("-trim",trim,arguments);
trim5 = angsd::getArg("-trim5",trim5,arguments);
trim3 = angsd::getArg("-trim3",trim3,arguments);
arguments->ref=angsd::getArg("-ref",arguments->ref,arguments);
arguments->anc=angsd::getArg("-anc",arguments->anc,arguments);
rghash_name= angsd::getArg("+RG",rghash_name,arguments);
if(rghash_name&&!angsd::fexists(rghash_name))
rghash = add_read_group_single(rghash_name);
if(rghash_name&&angsd::fexists(rghash_name))
rghash = add_read_groups_file(rghash_name);
if(rghash)
fprintf(stderr,"\t-> [READGROUP info] Number of readgroups to include: %d\n",khash_str2int_size(rghash));
adjustMapQ = angsd::getArg("-C",adjustMapQ,arguments);
baq = angsd::getArg("-baq",baq,arguments);
redo_baq = angsd::getArg("-redo-baq",redo_baq,arguments);
if(baq){
if(baq==1)
baq=1; //wauv
else if(baq==2)
baq=3;
else{
fprintf(stderr,"\t-> only supported options for -baq is: 1 (normal baq) and 2 (extended baq (SAMtools default)). Value supplied:%d\n",baq);
exit(0);//ly su
}
if(redo_baq==1)
baq |=4;
}
// fprintf(stderr,"baq:%d redobaq:%d\n",baq,redo_baq);exit(0);
regfile =angsd::getArg("-r",regfile,arguments);
regfiles = angsd::getArg("-rf",regfiles,arguments);
MAX_SEQ_LEN = angsd::getArg("-setMinChunkSize",MAX_SEQ_LEN,arguments);
checkBamHeaders = angsd::getArg("-checkBamHeaders",checkBamHeaders,arguments);
doCheck = angsd::getArg("-doCheck",doCheck,arguments);
MPLP_IGNORE_RG = angsd::getArg("--ignore-RG",MPLP_IGNORE_RG,arguments);
arguments->nReads = angsd::getArg("-nReads",arguments->nReads,arguments);
arguments->show = angsd::getArg("-show",arguments->show,arguments);
if(regfile && regfiles)
fprintf(stderr,"\t-> WARNING both -r and -rf has been set \n");
if(seed)
srand48(seed);
char *tmp = NULL;
tmp = angsd::getArg("-ref",tmp,arguments);
if(tmp==NULL && adjustMapQ!=0){
fprintf(stderr,"\t-> Must also supply -ref for adjusting the mapping quality\n");
exit(0);
}
if(tmp==NULL&&baq!=0){
fprintf(stderr,"\t-> Must also supply -ref for adjusting base qualities (baq)\n");
exit(0);
}
free(tmp);
std::vector<char *> regionsRaw;
if(regfiles)
regionsRaw = angsd::getFilenames(regfiles,0);
if(regfile)
regionsRaw.push_back(strdup(regfile));
// fprintf(stderr,"\t-> RegionsRaw.size():%lu hd:%p\n",regionsRaw.size(),arguments->hd);
for(size_t i=0;i<regionsRaw.size();i++){
regs tmpRegs;
if(parse_region(regionsRaw[i],arguments->hd,tmpRegs.refID,tmpRegs.start,tmpRegs.stop,arguments->revMap)<0||tmpRegs.stop<tmpRegs.start){
fprintf(stderr,"[%s] Problems with indexing: %s\n",__FUNCTION__,regionsRaw[i]);
exit(0);
}else
arguments->regions.push_back(tmpRegs);
free(regionsRaw[i]);
}
printArg(arguments->argumentFile,arguments);
if(regfile)
free(regfile);
if(regfiles)
free(regfiles);
}
/*
The logic of this function is a bit complicated because we want to work
also with broken bams containing read groups that are not listed in the
header. The desired behavior is as follows:
- when -G is given, read groups which are not listed in the header must
be given explicitly using the "?" symbol in -G.
Otherwise:
- if the bam has no header, all reads in the file are assigned to a
single sample named after the file
- if there is at least one sample defined in the header, reads with no
read group id or with a read group id not listed in the header are
assigned to the first sample encountered in the header
*/
int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname)
{
bsmpl->nfiles++;
bsmpl->files = (file_t*) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t));
file_t *file = &bsmpl->files[bsmpl->nfiles-1];
memset(file,0,sizeof(file_t));
file->fname = strdup(fname);
file->default_idx = -1;
if ( bsmpl->ignore_rg || !bam_hdr )
{
// The option --ignore-RG is set or there is no BAM header: use the file name as the sample name
bsmpl_add_readgroup(bsmpl,file,"*",file->fname);
return bsmpl->nfiles-1;
}
void *bam_smpls = khash_str2int_init();
int first_smpl = -1, nskipped = 0;
const char *p = bam_hdr, *q, *r;
while (p != NULL && (q = strstr(p, "@RG")) != 0)
{
char *eol = strchr(q + 3, '\n');
if (q > bam_hdr && *(q - 1) != '\n') { // @RG must be at start of line
p = eol;
continue;
}
p = q + 3;
if ((q = strstr(p, "\tID:")) != 0) q += 4;
if ((r = strstr(p, "\tSM:")) != 0) r += 4;
if (r && q)
{
char *u, *v;
int ioq, ior;
for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
ioq = *u; ior = *v; *u = *v = '\0';
// q now points to a null terminated read group id
// r points to a null terminated sample name
if ( !strcmp("*",q) || !strcmp("?",q) )
error("Error: the read group IDs \"*\" and \"?\" have a special meaning in the mpileup code. Please fix the code or the bam: %s\n", fname);
int accept_rg = 1;
if ( bsmpl->sample_list )
{
// restrict samples based on the -s/-S options
char *name = khash_str2str_get(bsmpl->sample_list,r);
if ( bsmpl->sample_logic==0 )
accept_rg = name ? 0 : 1;
else if ( !name )
accept_rg = 0;
else
r = name;
}
if ( accept_rg && bsmpl->rg_list )
{
// restrict readgroups based on the -G option, possibly renaming the sample
accept_rg = bsmpl_keep_readgroup(bsmpl,file,q,&r);
}
if ( accept_rg )
bsmpl_add_readgroup(bsmpl,file,q,r);
else
{
bsmpl_add_readgroup(bsmpl,file,q,NULL); // ignore this RG but note that it was seen in the header
nskipped++;
}
if ( first_smpl<0 )
khash_str2int_get(bsmpl->name2idx,r,&first_smpl);
if ( !khash_str2int_has_key(bam_smpls,r) )
khash_str2int_inc(bam_smpls,strdup(r));
*u = ioq; *v = ior;
}
else
break;
p = eol;
}
int nsmpls = khash_str2int_size(bam_smpls);
khash_str2int_destroy_free(bam_smpls);
const char *smpl_name = NULL;
int accept_null_rg = 1;
if ( bsmpl->rg_list && !bsmpl_keep_readgroup(bsmpl,file,"?",&smpl_name) ) accept_null_rg = 0;
if ( bsmpl->sample_list && first_smpl==-1 ) accept_null_rg = 0;
if ( !accept_null_rg && first_smpl==-1 )
{
// no suitable read group is available in this bam: ignore the whole file.
free(file->fname);
if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx);
bsmpl->nfiles--;
return -1;
}
if ( !accept_null_rg ) return bsmpl->nfiles-1;
if ( nsmpls==1 && !nskipped )
{
file->default_idx = first_smpl;
return bsmpl->nfiles-1;
}
if ( !smpl_name ) smpl_name = first_smpl==-1 ? file->fname : bsmpl->smpl[first_smpl];
bsmpl_add_readgroup(bsmpl,file,"?",smpl_name);
return bsmpl->nfiles-1;
}
