diff --git a/src/correction/generateCorrectionLayouts.C b/src/correction/generateCorrectionLayouts.C index 5095a092a..be1fd2541 100644 --- a/src/correction/generateCorrectionLayouts.C +++ b/src/correction/generateCorrectionLayouts.C @@ -181,7 +181,6 @@ main(int argc, char **argv) { bool doLogging = false; uint32 expectedCoverage = 40; // How many overlaps per read to save, global filter - uint32 minEvidenceOverlap = 40; uint32 iidMin = 1; uint32 iidMax = UINT32_MAX; @@ -212,19 +211,22 @@ main(int argc, char **argv) { } else if (strcmp(argv[arg], "-b") == 0) { // READ SELECTION - iidMin = atoi(argv[++arg]); + iidMin = strtouint32(argv[++arg]); } else if (strcmp(argv[arg], "-e") == 0) { - iidMax = atoi(argv[++arg]); + iidMax = strtouint32(argv[++arg]); } else if (strcmp(argv[arg], "-eL") == 0) { // EVIDENCE SELECTION - minEvidenceLength = atoi(argv[++arg]); + minEvidenceLength = strtouint32(argv[++arg]); } else if (strcmp(argv[arg], "-eE") == 0) { - maxEvidenceErate = atof(argv[++arg]); + maxEvidenceErate = strtodouble(argv[++arg]); } else if (strcmp(argv[arg], "-eC") == 0) { - maxEvidenceCoverage = atof(argv[++arg]); + maxEvidenceCoverage = strtodouble(argv[++arg]); + + } else if (strcmp(argv[arg], "-xC") == 0) { + expectedCoverage = strtouint32(argv[++arg]); } else if (strcmp(argv[arg], "-V") == 0) { doLogging = true; @@ -232,7 +234,6 @@ main(int argc, char **argv) { } else if (strcmp(argv[arg], "-D") == 0) { dumpScores = true; - } else { fprintf(stderr, "ERROR: unknown option '%s'\n", argv[arg]); err++; @@ -268,6 +269,8 @@ main(int argc, char **argv) { fprintf(stderr, " -eE erate maximum error rate of evidence overlaps\n"); fprintf(stderr, " -eC coverage maximum coverage of evidence reads to emit\n"); fprintf(stderr, "\n"); + fprintf(stderr, " -xC coverage estimated coverage in input reads\n"); + fprintf(stderr, "\n"); if (seqName == NULL) fprintf(stderr, "ERROR: no input seqStore (-S) supplied.\n");