runtime·malg(int32 stacksize)
{
G *newg;
byte *stk;
if(StackTop < sizeof(Stktop)) {
runtime·printf("runtime: SizeofStktop=%d, should be >=%d\n", (int32)StackTop, (int32)sizeof(Stktop));
runtime·throw("runtime: bad stack.h");
}
newg = runtime·malloc(sizeof(G));
if(stacksize >= 0) {
if(g == m->g0) {
// running on scheduler stack already.
stk = runtime·stackalloc(StackSystem + stacksize);
} else {
// have to call stackalloc on scheduler stack.
g->param = (void*)(StackSystem + stacksize);
runtime·mcall(mstackalloc);
stk = g->param;
g->param = nil;
}
newg->stack0 = stk;
newg->stackguard = stk + StackGuard;
newg->stackbase = stk + StackSystem + stacksize - sizeof(Stktop);
runtime·memclr(newg->stackbase, sizeof(Stktop));
}
return newg;
}
runtime·MHeap_Alloc(MHeap *h, uintptr npage, int32 sizeclass, bool large, bool needzero)
{
MSpan *s;
// Don't do any operations that lock the heap on the G stack.
// It might trigger stack growth, and the stack growth code needs
// to be able to allocate heap.
if(g == g->m->g0) {
s = mheap_alloc(h, npage, sizeclass, large);
} else {
g->m->ptrarg[0] = h;
g->m->scalararg[0] = npage;
g->m->scalararg[1] = sizeclass;
g->m->scalararg[2] = large;
runtime·mcall(mheap_alloc_m);
s = g->m->ptrarg[0];
g->m->ptrarg[0] = nil;
}
if(s != nil) {
if(needzero && s->needzero)
runtime·memclr((byte*)(s->start<<PageShift), s->npages<<PageShift);
s->needzero = 0;
}
return s;
}
void
runtime·gosched(void)
{
if(m->locks != 0)
runtime·throw("gosched holding locks");
if(g == m->g0)
runtime·throw("gosched of g0");
runtime·mcall(schedule);
}
// The implementation of the predeclared function panic.
void
runtime·panic(Eface e)
{
Defer *d;
Panic *p;
void *pc, *argp;
p = runtime·mal(sizeof *p);
p->arg = e;
p->link = g->panic;
p->stackbase = g->stackbase;
g->panic = p;
for(;;) {
d = g->defer;
if(d == nil)
break;
// take defer off list in case of recursive panic
g->defer = d->link;
g->ispanic = true; // rock for newstack, where reflect.newstackcall ends up
argp = d->argp;
pc = d->pc;
runtime·newstackcall(d->fn, (byte*)d->args, d->siz);
freedefer(d);
if(p->recovered) {
g->panic = p->link;
if(g->panic == nil) // must be done with signal
g->sig = 0;
runtime·free(p);
// Pass information about recovering frame to recovery.
g->sigcode0 = (uintptr)argp;
g->sigcode1 = (uintptr)pc;
runtime·mcall(recovery);
runtime·throw("recovery failed"); // mcall should not return
}
}
// ran out of deferred calls - old-school panic now
runtime·startpanic();
printpanics(g->panic);
runtime·dopanic(0);
}
// The implementation of the predeclared function panic.
void
runtime·panic(Eface e)
{
Defer *d;
Panic *p;
p = runtime·mal(sizeof *p);
p->arg = e;
p->link = g->panic;
p->stackbase = g->stackbase;
g->panic = p;
for(;;) {
d = g->defer;
if(d == nil)
break;
// take defer off list in case of recursive panic
g->defer = d->link;
g->ispanic = true; // rock for newstack, where reflect.call ends up
reflect·call(d->fn, d->args, d->siz);
if(p->recovered) {
g->panic = p->link;
if(g->panic == nil) // must be done with signal
g->sig = 0;
runtime·free(p);
// put recovering defer back on list
// for scheduler to find.
d->link = g->defer;
g->defer = d;
runtime·mcall(recovery);
runtime·throw("recovery failed"); // mcall should not return
}
if(!d->nofree)
runtime·free(d);
}
// ran out of deferred calls - old-school panic now
runtime·startpanic();
printpanics(g->panic);
runtime·dopanic(0);
}
runtime·malg(int32 stacksize)
{
G *newg;
byte *stk;
newg = runtime·malloc(sizeof(G));
if(stacksize >= 0) {
if(g == m->g0) {
// running on scheduler stack already.
stk = runtime·stackalloc(StackSystem + stacksize);
} else {
// have to call stackalloc on scheduler stack.
g->param = (void*)(StackSystem + stacksize);
runtime·mcall(mstackalloc);
stk = g->param;
g->param = nil;
}
newg->stack0 = stk;
newg->stackguard = stk + StackGuard;
newg->stackbase = stk + StackSystem + stacksize - sizeof(Stktop);
runtime·memclr(newg->stackbase, sizeof(Stktop));
}
return newg;
}
int main_vcfcall(int argc, char *argv[])
{
char *samples_fname = NULL;
args_t args;
memset(&args, 0, sizeof(args_t));
args.argc = argc; args.argv = argv;
args.aux.prior_type = -1;
args.aux.indel_frac = -1;
args.aux.theta = 1e-3;
args.aux.pref = 0.5;
args.aux.min_perm_p = 0.01;
args.aux.min_lrt = 1;
args.flag = CF_ACGT_ONLY;
args.output_fname = "-";
args.output_type = FT_VCF;
args.aux.trio_Pm_SNPs = 1 - 1e-8;
args.aux.trio_Pm_ins = args.aux.trio_Pm_del = 1 - 1e-9;
int i, c, samples_is_file = 0;
static struct option loptions[] =
{
{"help",0,0,'h'},
{"gvcf",1,0,'g'},
{"format-fields",1,0,'f'},
{"output",1,0,'o'},
{"output-type",1,0,'O'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"samples",1,0,'s'},
{"samples-file",1,0,'S'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"keep-alts",0,0,'A'},
{"insert-missed",0,0,'i'},
{"skip-Ns",0,0,'N'}, // now the new default
{"keep-masked-refs",0,0,'M'},
{"skip-variants",1,0,'V'},
{"variants-only",0,0,'v'},
{"consensus-caller",0,0,'c'},
{"constrain",1,0,'C'},
{"multiallelic-caller",0,0,'m'},
{"pval-threshold",1,0,'p'},
{"prior",1,0,'P'},
{"chromosome-X",0,0,'X'},
{"chromosome-Y",0,0,'Y'},
{"novel-rate",1,0,'n'},
{0,0,0,0}
};
char *tmp = NULL;
while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:XYn:P:f:ig:", loptions, NULL)) >= 0)
{
switch (c)
{
case 'g':
args.flag |= CF_GVCF;
args.gvcf.min_dp = strtol(optarg,&tmp,10);
if ( *tmp ) error("Could not parse, expected integer argument: -g %s\n", optarg);
break;
case 'f': args.aux.output_tags |= parse_format_flag(optarg); break;
case 'M': args.flag &= ~CF_ACGT_ONLY; break; // keep sites where REF is N
case 'N': args.flag |= CF_ACGT_ONLY; break; // omit sites where first base in REF is N (the new default)
case 'A': args.aux.flag |= CALL_KEEPALT; break;
case 'c': args.flag |= CF_CCALL; break; // the original EM based calling method
case 'i': args.flag |= CF_INS_MISSED; break;
case 'v': args.aux.flag |= CALL_VARONLY; break;
case 'o': args.output_fname = optarg; break;
case 'O':
switch (optarg[0]) {
case 'b': args.output_type = FT_BCF_GZ; break;
case 'u': args.output_type = FT_BCF; break;
case 'z': args.output_type = FT_VCF_GZ; break;
case 'v': args.output_type = FT_VCF; break;
default: error("The output type \"%s\" not recognised\n", optarg);
}
break;
case 'C':
if ( !strcasecmp(optarg,"alleles") ) args.aux.flag |= CALL_CONSTR_ALLELES;
else if ( !strcasecmp(optarg,"trio") ) args.aux.flag |= CALL_CONSTR_TRIO;
else error("Unknown argument to -C: \"%s\"\n", optarg);
break;
case 'X': args.aux.flag |= CALL_CHR_X; break;
case 'Y': args.aux.flag |= CALL_CHR_Y; break;
case 'V':
if ( !strcasecmp(optarg,"snps") ) args.flag |= CF_INDEL_ONLY;
else if ( !strcasecmp(optarg,"indels") ) args.flag |= CF_NO_INDEL;
else error("Unknown skip category \"%s\" (-S argument must be \"snps\" or \"indels\")\n", optarg);
break;
case 'm': args.flag |= CF_MCALL; break; // multiallelic calling method
case 'p': args.aux.pref = atof(optarg); break;
case 'P': args.aux.theta = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse, expected float argument: -P %s\n", optarg);
break;
case 'n': parse_novel_rate(&args,optarg); break;
case 'r': args.regions = optarg; break;
case 'R': args.regions = optarg; args.regions_is_file = 1; break;
case 't': args.targets = optarg; break;
case 'T': args.targets = optarg; args.targets_is_file = 1; break;
case 's': samples_fname = optarg; break;
case 'S': samples_fname = optarg; samples_is_file = 1; break;
default: usage(&args);
}
}
if ( optind>=argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-"; // reading from stdin
else usage(&args);
}
else args.bcf_fname = argv[optind++];
// Sanity check options and initialize
if ( samples_fname )
{
args.samples = read_samples(&args.aux, samples_fname, samples_is_file, &args.nsamples);
args.aux.ploidy = (uint8_t*) calloc(args.nsamples+1, 1);
args.aux.all_diploid = 1;
for (i=0; i<args.nsamples; i++)
{
args.aux.ploidy[i] = args.samples[i][strlen(args.samples[i]) + 1];
if ( args.aux.ploidy[i]!=2 ) args.aux.all_diploid = 0;
}
}
if ( args.flag & CF_GVCF )
{
// Force some flags to avoid unnecessary branching
args.aux.flag &= ~CALL_KEEPALT;
args.aux.flag |= CALL_VARONLY;
}
if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n");
if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n");
if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n"); // not sure about this, please fix
if ( args.aux.flag & CALL_CONSTR_ALLELES )
{
if ( !args.targets ) error("Expected -t or -T with \"-C alleles\"\n");
if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n");
}
if ( args.aux.flag & CALL_CHR_X && args.aux.flag & CALL_CHR_Y ) error("Only one of -X or -Y should be given\n");
if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n");
init_data(&args);
while ( bcf_sr_next_line(args.aux.srs) )
{
bcf1_t *bcf_rec = args.aux.srs->readers[0].buffer[0];
if ( args.samples_map ) bcf_subset(args.aux.hdr, bcf_rec, args.nsamples, args.samples_map);
bcf_unpack(bcf_rec, BCF_UN_STR);
// Skip unwanted sites
if ( args.aux.flag & CALL_VARONLY )
{
int is_ref = 0;
if ( bcf_rec->n_allele==1 ) is_ref = 1; // not a variant
else if ( bcf_rec->n_allele==2 )
{
// second allele is mpileup's X, not a variant
if ( bcf_rec->d.allele[1][0]=='X' ) is_ref = 1;
else if ( bcf_rec->d.allele[1][0]=='<' && bcf_rec->d.allele[1][1]=='X' && bcf_rec->d.allele[1][2]=='>' ) is_ref = 1;
}
if ( is_ref )
{
// gVCF output
if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, 1);
continue;
}
}
if ( (args.flag & CF_INDEL_ONLY) && bcf_is_snp(bcf_rec) ) continue; // not an indel
if ( (args.flag & CF_NO_INDEL) && !bcf_is_snp(bcf_rec) ) continue; // not a SNP
if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue; // REF[0] is 'N'
bcf_unpack(bcf_rec, BCF_UN_ALL);
// Various output modes: QCall output (todo)
if ( args.flag & CF_QCALL )
{
qcall(&args.aux, bcf_rec);
continue;
}
// Calling modes which output VCFs
int ret;
if ( args.flag & CF_MCALL )
ret = mcall(&args.aux, bcf_rec);
else
ret = ccall(&args.aux, bcf_rec);
if ( ret==-1 ) error("Something is wrong\n");
// gVCF output
if ( args.flag & CF_GVCF )
{
gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, ret?0:1);
continue;
}
// Normal output
if ( (args.aux.flag & CALL_VARONLY) && ret==0 ) continue; // not a variant
bcf_write1(args.out_fh, args.aux.hdr, bcf_rec);
}
if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, NULL, 0);
if ( args.flag & CF_INS_MISSED ) bcf_sr_regions_flush(args.aux.srs->targets);
destroy_data(&args);
return 0;
}
