void read_token()
{
clear_variant(&value);
token = next_token;
value = next_value;
init_variant(&next_value);
next_token = scan_token(&next_value);
}
int parse(const char* file, program_t* p)
{
int r = 0;
FILE* fp = NULL;
prog = p;
prog->file = strdup(file);
assert(prog != NULL);
if (file != NULL)
{
fp = fopen(file, "r");
if (fp == NULL)
{
fprintf(stderr, "Failed to open %s\n", file);
return -1;
}
}
else
{
fp = stdin;
file = "<stdin>";
}
r = start_scan(fp, file);
if (r < 0)
{
return r;
}
init_variant(&value);
init_variant(&next_value);
next_token = scan_token(&next_value);
read_program();
return result;
}
void read_argument(arg_t* arg)
{
assert(arg != NULL);
int as_value = 0;
unsigned int t1 = 0;
variant_t v1;
unsigned int t2 = 0;
init_variant(&v1);
read_token();
if (token == LEFT_BRAKET_TOKEN)
{
as_value = 1;
read_token();
}
else
{
as_value = 0;
}
if (is_value_token(token))
{
t1 = token;
copy_variant(&v1, &value);
}
else
{
fprintf(stderr, "%s:%d: error: Expected identifier or integer but got %s.\n", get_scan_file(), get_scan_line(), get_token_name(token));
result = -1;
return;
}
if (next_token == PLUS_TOKEN)
{
read_token();
assert(token == PLUS_TOKEN);
read_token();
if (is_value_token(token))
{
t2 = token;
}
else
{
fprintf(stderr, "%s:%d: error: Expected identifier or integer but got %s.\n", get_scan_file(), get_scan_line(), get_token_name(token));
result = -1;
return;
}
}
if (as_value == 1)
{
read_token();
if (token != RIGHT_BRAKET_TOKEN)
{
fprintf(stderr, "%s:%d: error: Missmatched braket.\n", get_scan_file(), get_scan_line());
result = -1;
return;
}
}
/*
0x00-0x07: register (A, B, C, X, Y, Z, I or J, in that order)
0x08-0x0f: [register]
0x10-0x17: [next word + register]
0x18: POP / [SP++]
0x19: PEEK / [SP]
0x1a: PUSH / [--SP]
0x1b: SP
0x1c: PC
0x1d: O
0x1e: [next word]
0x1f: next word (literal)
0x20-0x3f: literal value 0x00-0x1f (literal)
*/
if (is_symbolic(t1))
{
switch (t1)
{
case A_TOKEN:
if (as_value)
arg->value = 0x08;
else
arg->value = 0x00;
break;
case B_TOKEN:
if (as_value)
arg->value = 0x09;
else
arg->value = 0x01;
break;
case C_TOKEN:
if (as_value)
arg->value = 0x0A;
else
arg->value = 0x02;
break;
case X_TOKEN:
if (as_value)
arg->value = 0x0B;
else
arg->value = 0x03;
break;
case Y_TOKEN:
if (as_value)
arg->value = 0x0C;
else
arg->value = 0x04;
break;
case Z_TOKEN:
if (as_value)
arg->value = 0x0D;
else
arg->value = 0x05;
break;
case I_TOKEN:
if (as_value)
arg->value = 0x0E;
else
arg->value = 0x06;
break;
case J_TOKEN:
if (as_value)
arg->value = 0x0F;
else
arg->value = 0x07;
break;
case POP_TOKEN:
arg->value = 0x18;
break;
case PEEK_TOKEN:
arg->value = 0x19;
break;
case PUSH_TOKEN:
arg->value = 0x1A;
break;
case SP_TOKEN:
arg->value = 0x1B;
break;
case PC_TOKEN:
arg->value = 0x1C;
break;
case O_TOKEN:
arg->value = 0x1D;
break;
}
/* TODO validate that there is no offset */
}
else if (t1 == IDENTIFIER_TOKEN)
{
// for jumps we encode alwas next word
// this is since we can't resolve the target at this point
arg->value = 0x1F;
copy_variant(&arg->extra, &v1);
/* TODO validate that there is no offset */
}
else
{
assert(t1 == INTEGER_TOKEN);
assert(v1.type == UINT_TYPE);
if (as_value && t2 == 0)
{
arg->value = 0x1E;
copy_variant(&arg->extra, &v1);
}
if (!as_value && t2 == 0)
{
if (v1.ui <= 0x1F)
{
arg->value = 0x20 + v1.ui;
}
else
{
arg->value = 0x1F;
copy_variant(&arg->extra, &v1);
}
}
if (t2 != 0)
{
assert(as_value == 1);
switch (t2)
{
case A_TOKEN:
arg->value = 0x10;
break;
case B_TOKEN:
arg->value = 0x11;
break;
case C_TOKEN:
arg->value = 0x12;
break;
case X_TOKEN:
arg->value = 0x13;
break;
case Y_TOKEN:
arg->value = 0x14;
break;
case Z_TOKEN:
arg->value = 0x15;
break;
case I_TOKEN:
arg->value = 0x16;
break;
case J_TOKEN:
arg->value = 0x17;
break;
default:
assert(0 && "should never happen");
break;
}
copy_variant(&arg->extra, &v1);
}
}
}
// multi sample variant caller: CRISP, PICALL or low coverage method
int multisampleVC(struct OPTIONS* options,REFLIST* reflist,FILE* fp)
{
if (USE_DUPLICATES ==1) BAM_FILTER_MASK = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL); else BAM_FILTER_MASK = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP);
int bamfiles = options->bamfiles;
int last=0; // last is the current position s.t. all reads have starting position > last
int i=0; int h=0;
unsigned long reads=0; int j=0; int prev_tid = -1; int rf=0;
int finishedfiles =0;
struct alignedread* pread = NULL;
struct BAMFILE_data* bamfiles_data = calloc(bamfiles,sizeof(struct BAMFILE_data)); // added one extra to list to store indels for all samples combined
READQUEUE* RQ = (READQUEUE*)malloc(sizeof(READQUEUE)); RQ->first = NULL; RQ->last = NULL; RQ->reads = 0;
int* fcigarlist = (int*)malloc(sizeof(int)*4096);
// data structure for holding potential variants and read counts, etc
struct VARIANT variant; variant.ploidy = calloc(options->bamfiles,sizeof(int));
init_poolsizes(&variant,options,PICALL);
init_variant(&variant,options->bamfiles,options->bamfiles);
variant.options = options; // pointer to options
BAMHEAP bheap; bheap.harray = (int*)malloc(sizeof(int)*bamfiles); bheap.length = bamfiles;
for (i=0;i<bamfiles;i++) { bheap.harray[i] = i; bamfiles_data[i].finished= 0;}
reflist->cinterval = -1; // first interval to the right of current base
init_bamfiles(bamfiles_data,options->bamfilelist,bamfiles,options->regions,&options->targettid,&options->targetstart,&options->targetend);
// error when reading indexed bam files probably due to lack of reads in some files resulting in heap error, fixed oct 17 2012
j=0; for (i=0;i<bamfiles;i++)
{
finishedfiles += bamfiles_data[i].finished;
if (bamfiles_data[i].finished ==0) bheap.harray[j++] = i; else bheap.length--;
}
buildminheap(&bheap,bamfiles_data); // initial minheap call
//fprintf(stderr,"finishedfiles %d \n",finishedfiles);
if (INDEL_REALIGNMENT >=1) allocate_mem_heap(bamfiles_data,bamfiles,100);
HAPLOTYPES =0,MIN_COVERAGE_FLANKING =0;
for (i=0;i<variant.samples;i++)
{
MIN_COVERAGE_FLANKING += 2*variant.ploidy[i]; // enforced for regions outside the bedfile target
HAPLOTYPES += variant.ploidy[i];
}
//int min_coverage_target = 1*variant->ploidy*variant->samples; // enforced for regions outside the bedfile target
int offset_readlength = 150; // call variants in window (last,current_read_position-offset_readlength) to allow for indel analysis, set to 0 for original behavior of program
// the value of offset should not affect the correctness or speed of the code
int current_position =0;
while (finishedfiles < bamfiles)
{
i = bheap.harray[0]; // take the top read off the heap
if ( !(bamfiles_data[i].read->flag & BAM_FILTER_MASK))
{
if (bamfiles_data[i].read->tid != prev_tid) // read's chromosome is different from previousread
{
if (prev_tid >=0) // finish the processing of previous chromosome and cleanup
{
if (RQ->reads >0)
{
fprintf(stderr,"processing %d reads left in queue for chrom %s...",RQ->reads,reflist->names[prev_tid]);
callvariants(reflist,prev_tid,last,reflist->lengths[prev_tid],RQ,bamfiles_data,options,&variant);
empty_queue(RQ,bamfiles_data); //clean thequeue
}
if (INDEL_REALIGNMENT >=1) clean_indel_lists(bamfiles_data,bamfiles,-1); current_position = 0;
for(j=0;j<bamfiles;j++) bamfiles_data[j].last=NULL; last =0;
free(reflist->sequences[prev_tid]);
fprintf(stderr,".....finished processing reads for chrom %s\n",reflist->names[prev_tid]);
fprintf(stdout,".....finished processing reads for chrom %s\n",reflist->names[prev_tid]);
reflist->cinterval = -1; // reset to -1
}
read_chromosome(reflist,bamfiles_data[i].read->tid,fp);
prev_tid =bamfiles_data[i].read->tid;
}
if (bamfiles_data[i].read->position <last)
{
fprintf(stderr,"reads out of order i:%d h:%d pos: %d %d\n",i,h,bamfiles_data[i].read->position,last);
fprintf(stderr,"the program will now exit, please sort the bamfiles\n");
return 1;
}
if (INDEL_REALIGNMENT >=1 && bamfiles_data[i].read->position > current_position+offset_readlength)
{
// need to clean up indel lists when we encounter a new chromosome...
print_indel_lists(bamfiles_data,bamfiles,current_position+offset_readlength);
clean_indel_lists(bamfiles_data,bamfiles,current_position);
current_position = bamfiles_data[i].read->position;
}
// realign reads before calling variants, each read is realigned only once
// small bug here, only call variants when last is less than current read position
// bug fixed here, update last only when 'callvariants' is invoked, ???
if (RQ->reads > 0 && bamfiles_data[i].read->position > last+offset_readlength)
{
callvariants(reflist,bamfiles_data[i].read->tid,last,bamfiles_data[i].read->position-offset_readlength,RQ,bamfiles_data,options,&variant);
}
last = bamfiles_data[i].read->position-offset_readlength; if (last < 0) last =0;
bamfiles_data[i].read->cflag = 0;
// this function should only be called on reads inside/close_to targeted regions..
parse_cigar(bamfiles_data[i].read,reflist,bamfiles_data[i].read->tid,fcigarlist);
if (INDEL_REALIGNMENT >=1 && bamfiles_data[i].read->gaps > 0 && bamfiles_data[i].read->mquality >= 20) extract_indel_reads(bamfiles_data[i].read,reflist,bamfiles_data[i].read->tid,i,bamfiles_data[i].ilist);
//fprintf(stdout,"read s:%d IS:%d %s %d \n",i,bamfiles_data[i].read->IS,bamfiles_data[i].read->readid,bamfiles_data[i].read->position);
if (RQ->last == NULL)
{
RQ->last = bamfiles_data[i].read; RQ->first = RQ->last; (RQ->last)->next = NULL;
RQ->reads++;
}
else
{
(RQ->last)->next = bamfiles_data[i].read; RQ->last = bamfiles_data[i].read;
(RQ->last)->next = NULL;
RQ->reads++;
}
if (bamfiles_data[i].last ==NULL) bamfiles_data[i].first = RQ->last;
else bamfiles_data[i].last->nextread= RQ->last;
bamfiles_data[i].last = RQ->last; (RQ->last)->nextread =NULL;
// read that passes filters from 'i'th bam file is inserted in queue, should also add it to OPE queue
//if (bamfiles_data[i].read->position < bamfiles_data[i].read->mateposition && bamfiles_data[i].read->lastpos > bamfiles_data[i].read->mateposition)
//fprintf(stdout,"B %d %s %d %d %d \n",i,bamfiles_data[i].read->readid,bamfiles_data[i].read->position,bamfiles_data[i].read->mateposition,bamfiles_data[i].read->IS);
}
else free_read(bamfiles_data[i].read);
//fprintf(stdout,"read from %d %d %s\n",i,bamfiles_data[i].read->position,bamfiles_data[i].read->readid);
if (options->regions ==NULL) rf =samread(bamfiles_data[i].fp,bamfiles_data[i].b);
else rf = bam_iter_read(bamfiles_data[i].fp->x.bam,bamfiles_data[i].iter,bamfiles_data[i].b);
if (rf >=0)
{
bamfiles_data[i].read = get_read_bamfile(bamfiles_data[i].b,bamfiles_data[i].fp,pread);
//if (options->samples ==0) bamfiles_data[i].read->sampleid = i;
//else bamfiles_data[i].read->sampleid = options->BAM_TO_SAMPLE[i];
// bug here june 30 2013 commented out .... in 12 T2D pools
bamfiles_data[i].read->sampleid = i;
if (!(bamfiles_data[i].read->flag & BAM_FILTER_MASK)) minHeapify(&bheap,0,bamfiles_data);
}
else // no more reads in file 'i'
{
bamfiles_data[i].finished = 1; bamfiles_data[i].read= NULL;
bam_destroy1(bamfiles_data[i].b);
h++; finishedfiles++;
//fprintf(stderr,"finished reading bam file %s \n",options->bamfilelist[i]); //return 1;
bheap.harray[0] = bheap.harray[bheap.length-1]; bheap.length--;
if (bheap.length > 0) minHeapify(&bheap,0,bamfiles_data);
// call minheapify like function to push sample i off the heap, reduce heap size
}
if ((++reads)%1000000 ==0 && RQ->reads >0) fprintf(stderr,".....processed %ld reads QSIZE:%d %s:%d:%d variants called %d\n",reads,RQ->reads,RQ->first->chrom,RQ->first->position,RQ->first->lastpos,VARIANTS_CALLED);
}
if (prev_tid >=0) // finish the processing of last chromosome
{
if (RQ->reads >0)
{
fprintf(stderr,"processing %d reads left in queue for chrom %s.....",RQ->reads,reflist->names[prev_tid]);
if (reflist->lengths[prev_tid] > last) callvariants(reflist,prev_tid,last,reflist->lengths[prev_tid],RQ,bamfiles_data,options,&variant);
empty_queue(RQ,bamfiles_data); //clean thequeue
}
else fprintf(stderr,"queue for chrom %s is empty ",reflist->names[prev_tid]);
free(reflist->sequences[prev_tid]);
fprintf(stderr,"finished processing reads for chrom %s \n\n",reflist->names[prev_tid]);
if (INDEL_REALIGNMENT >=1)
{
print_indel_lists(bamfiles_data,bamfiles,reflist->lengths[prev_tid]);
clean_indel_lists(bamfiles_data,bamfiles,reflist->lengths[prev_tid]);
}
}
fprintf(stderr,"CRISP has finished processing bam files: total reads processed %ld total variants called %d \n\n",reads,VARIANTS_CALLED);
//for (i=0;i<bamfiles;i++) bam_destroy1(bamfiles_data[i].b);
free(bamfiles_data); free(bheap.harray); free(fcigarlist);
//empty_queue(RQ); //clean thequeue
//fprintf(stdout,"FILE %d %s %d %s %d %d %d mapped %d \n",i,read->readid,read->flag,read->chrom,read->position,read->mquality,read->IS,(read->flag &4));
return 1;
}