#include #include #include #include "easyTrackCache.h" int main(int argc, char *argv[]) { int result; int start, end, width; int geneThreshold; int optSelectFlag, optRealFlag; double realLower, realUpper; if (!((argc == 10) || (argc == 17))) { fprintf(stderr, "-------------------------------------------------------------------------\n"); fprintf(stderr, "usage: %s name species revision target start end width outputfile threshold\n", argv[0]); fprintf(stderr, " OptSelectFlag SelectName SelectParam OptRealFlag RealName RealLower RealUpper\n"); fprintf(stderr, " ex) %s mappedGene medaka 200406 scaffold1 100 1000000 800 stdout 100\n", argv[0]); fprintf(stderr, " 1 fromSpecies medaka 1 matchRatio 0.99 1.0\n"); fprintf(stderr, "-------------------------------------------------------------------------\n"); exit(0); } start = atoi(argv[5]); end = atoi(argv[6]); width = atoi(argv[7]); geneThreshold = atoi(argv[9]); if (argc == 10) { result = getGeneData(argv[1], argv[2], argv[3], argv[4], start, end, width, NULL, argv[8], geneThreshold, 0, NULL, NULL, 0, NULL, 0.0, 0.0); } else { optSelectFlag = atoi(argv[10]); optRealFlag = atoi(argv[13]); realLower = atof(argv[15]); realUpper = atof(argv[16]); result = getGeneData(argv[1], argv[2], argv[3], argv[4], start, end, width, NULL, argv[8], geneThreshold, optSelectFlag, argv[11], argv[12], optRealFlag, argv[14], realLower, realUpper); } if (result) fprintf(stderr, "done.\n"); else fprintf(stderr, "error.\n"); checkAllocationCount(); exit(0); }