READ_INT_TYPE nUnique, nMulti, nIsoMulti;
char fn_list[STRLEN];
char groupF[STRLEN], tiF[STRLEN];
-char imdName[STRLEN];
char datF[STRLEN], cntF[STRLEN];
GroupInfo gi;
bool quiet = false;
if (argc < 6) {
- printf("Usage : rsem-parse-alignments refName sampleName sampleToken alignFType('s' for sam, 'b' for bam) alignF [-t Type] [-l fn_list] [-tag tagName] [-q]\n");
+ printf("Usage : rsem-parse-alignments refName imdName statName alignFType('s' for sam, 'b' for bam) alignF [-t Type] [-l fn_list] [-tag tagName] [-q]\n");
exit(-1);
}
sprintf(tiF, "%s.ti", argv[1]);
transcripts.readFrom(tiF);
- sprintf(imdName, "%s.temp/%s", argv[2], argv[3]);
- sprintf(datF, "%s.dat", imdName);
- sprintf(cntF, "%s.stat/%s.cnt", argv[2], argv[3]);
+ sprintf(datF, "%s.dat", argv[2]);
+ sprintf(cntF, "%s.cnt", argv[3]);
- init(imdName, argv[4][0], argv[5]);
+ init(argv[2], argv[4][0], argv[5]);
hit_out.open(datF);