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filter.c
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filter.c
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#include "generic.h"
int filter_usage(){
fprintf(stderr, "\n");
fprintf(stderr, "Obtain alignment statistics of individual loci of each repeat subfamily, family or class.\n\n");
fprintf(stderr, "Usage: iteres filter [options] <chromosome size file> <repeat size file> <rmsk.txt> <bam/sam alignment file>\n\n");
fprintf(stderr, "Options: -S input is SAM [off]\n");
fprintf(stderr, " -Q mapping Quality threshold [10]\n");
fprintf(stderr, " -g coverage threshold for overlapping [0.0001]\n");
fprintf(stderr, " -N normalized by number of (0: non-redundant unique mapped reads, 1: unique reads, 2: mapped reads, 3: total reads) [0])\n");
fprintf(stderr, " -n use repName (subfamily) as filter [null]\n");
fprintf(stderr, " -f use repFamily as filter [null]\n");
fprintf(stderr, " -c use repClass as filter [null]\n");
fprintf(stderr, " -t only output repeats have more than [1] reads mapped\n");
fprintf(stderr, " -r output the list of reads [off]\n");
fprintf(stderr, " -R remove redundant reads [off]\n");
fprintf(stderr, " -T treat 1 paired-end read as 2 single-end reads [off]\n");
fprintf(stderr, " -D discard if only one end mapped in a paired end reads [off]\n");
fprintf(stderr, " -C Add 'chr' string as prefix of reference sequence [off]\n");
fprintf(stderr, " -E extend reads to represent fragment [150], specify 0 if want no extension\n");
fprintf(stderr, " -I Insert length threshold [500]\n");
fprintf(stderr, " -o output prefix [basename of input without extension]\n");
fprintf(stderr, " -h help message\n");
fprintf(stderr, " -? help message\n");
fprintf(stderr, "\n");
return 1;
}
/* main filter function */
int main_filter(int argc, char *argv[]){
char *output, *subfam, *out, *outReport;
unsigned long long int *cnt;
struct hash *hashRmsk = newHash(0);
struct hash *hashRep = newHash(0);
struct hash *hashFam = newHash(0);
struct hash *hashCla = newHash(0);
int optSam = 0, optthreshold = 1;
char *optoutput = NULL, *optname = NULL, *optclass = NULL, *optfamily = NULL;
unsigned int optreadlist = 0, optQual = 10, optisize = 500, optExt = 150;
int filterField = 0, c, optDup = 0, optNorm = 0, optaddChr = 0, optDis =0, optTreat = 0;
float optCov = 0.0001;
time_t start_time, end_time;
start_time = time(NULL);
while ((c = getopt(argc, argv, "SQ:g:N:n:c:t:f:rRTDCE:I:o:h?")) >= 0) {
switch (c) {
case 'S': optSam = 1; break;
case 'Q': optQual = (unsigned int)strtol(optarg, 0, 0); break;
case 'g': optCov = atof(optarg); break;
case 'N': optNorm = (unsigned int)strtol(optarg, 0, 0); break;
case 't': optthreshold = (unsigned int)strtol(optarg, 0, 0); break;
case 'r': optreadlist = 1; break;
case 'R': optDup = 1; break;
case 'T': optTreat = 1; break;
case 'D': optDis = 1; break;
case 'C': optaddChr = 1; break;
case 'n': optname = strdup(optarg); break;
case 'c': optclass = strdup(optarg); break;
case 'f': optfamily = strdup(optarg); break;
case 'E': optExt = (unsigned int)strtol(optarg, 0, 0); break;
case 'I': optisize = (unsigned int)strtol(optarg, 0, 0); break;
case 'o': optoutput = strdup(optarg); break;
case 'h':
case '?': return filter_usage(); break;
default: return 1;
}
}
if (optind + 4 > argc)
return filter_usage();
char *chr_size_file = argv[optind];
char *rep_size_file = argv[optind+1];
char *rmsk_file = argv[optind+2];
char *sam_file = argv[optind+3];
if ( (optname && optclass) || (optname && optfamily) || (optclass && optfamily) || (optname && optclass && optfamily))
errAbort("Please specify only one filter, either -n, -c or -f.");
int nindex = 0;
if (optNorm == 0){
nindex = 7;
} else if (optNorm == 1){
nindex = 8;
} else if (optNorm == 2) {
nindex = 6;
} else if (optNorm == 3) {
nindex = 4;
} else{
errAbort("Wrong normalization method specified");
}
subfam = cloneString("ALL");
if (optname) {
optclass = NULL;
optfamily = NULL;
subfam = cloneString(optname);
filterField = 10;
}else if (optclass) {
optname = NULL;
optfamily = NULL;
subfam = cloneString(optclass);
filterField = 11;
} else if (optfamily) {
optname = NULL;
optclass= NULL;
subfam = cloneString(optfamily);
filterField = 12;
}
if (sameString(subfam, "ALL")){
fprintf(stderr, "* You didn't specify any filter, will output all repeats\n");
filterField = 0;
}
if(optoutput) {
output = optoutput;
} else {
output = cloneString(get_filename_without_ext(basename(sam_file)));
}
struct hash *chrHash = hashNameIntFile(chr_size_file);
struct hash *repHash = hashNameIntFile(rep_size_file);
fprintf(stderr, "* Start to parse the rmsk file\n");
rmsk2binKeeperHash(rmsk_file, chrHash, repHash, &hashRmsk, &hashRep, &hashFam, &hashCla, filterField, subfam);
//sam file
fprintf(stderr, "* Start to parse the SAM/BAM file\n");
//if (optPair){
// cnt = PEsamFile2nodupRepbedFile(sam_file, chrHash, hashRmsk, hashRep, hashFam, hashCla, optSam, optQual, 1, optDup, optaddChr, optisize);
//} else {
// cnt = samFile2nodupRepbedFile(sam_file, chrHash, hashRmsk, hashRep, hashFam, hashCla, optSam, optQual, 1, optDup, optaddChr);
//}
cnt = samFile2nodupRepbedFileNew(sam_file, chrHash, hashRmsk, hashRep, hashFam, hashCla, optSam, optQual, 1, optDup, optaddChr, optDis, optisize, optExt, optCov, optTreat, NULL, NULL, 0);
fprintf(stderr, "* Preparing the output file\n");
if (asprintf(&out, "%s_%s.iteres.loci", output, subfam) < 0)
errAbort("Preparing output wrong");
if (asprintf(&outReport, "%s_%s.iteres.reportloci", output, subfam) < 0)
errAbort("Preparing output wrong");
writeFilterOut(hashRmsk, out, optreadlist, optthreshold, subfam, cnt[nindex]);
//write report file
fprintf(stderr, "* Preparing report file\n");
writeReport(outReport, cnt, optQual, subfam);
hashFree(&chrHash);
hashFree(&repHash);
hashFree(&hashRmsk);
hashFree(&hashRep);
hashFree(&hashFam);
hashFree(&hashCla);
free(out);
free(outReport);
end_time = time(NULL);
fprintf(stderr, "* Done, time used %.0f seconds.\n", difftime(end_time, start_time));
return 0;
}