+10
-7
lines changedFilter options
+10
-7
lines changed Original file line number Diff line number Diff line change
@@ -181,7 +181,6 @@ main(int argc, char **argv) {
181 181
bool doLogging = false;
182 182 183 183
uint32 expectedCoverage = 40; // How many overlaps per read to save, global filter
184 -
uint32 minEvidenceOverlap = 40;
185 184 186 185
uint32 iidMin = 1;
187 186
uint32 iidMax = UINT32_MAX;
@@ -212,27 +211,29 @@ main(int argc, char **argv) {
212 211 213 212 214 213
} else if (strcmp(argv[arg], "-b") == 0) { // READ SELECTION
215 -
iidMin = atoi(argv[++arg]);
214 +
iidMin = strtouint32(argv[++arg]);
216 215 217 216
} else if (strcmp(argv[arg], "-e") == 0) {
218 -
iidMax = atoi(argv[++arg]);
217 +
iidMax = strtouint32(argv[++arg]);
219 218 220 219
} else if (strcmp(argv[arg], "-eL") == 0) { // EVIDENCE SELECTION
221 -
minEvidenceLength = atoi(argv[++arg]);
220 +
minEvidenceLength = strtouint32(argv[++arg]);
222 221 223 222
} else if (strcmp(argv[arg], "-eE") == 0) {
224 -
maxEvidenceErate = atof(argv[++arg]);
223 +
maxEvidenceErate = strtodouble(argv[++arg]);
225 224 226 225
} else if (strcmp(argv[arg], "-eC") == 0) {
227 -
maxEvidenceCoverage = atof(argv[++arg]);
226 +
maxEvidenceCoverage = strtodouble(argv[++arg]);
227 + 228 +
} else if (strcmp(argv[arg], "-xC") == 0) {
229 +
expectedCoverage = strtouint32(argv[++arg]);
228 230 229 231
} else if (strcmp(argv[arg], "-V") == 0) {
230 232
doLogging = true;
231 233 232 234
} else if (strcmp(argv[arg], "-D") == 0) {
233 235
dumpScores = true;
234 236 235 - 236 237
} else {
237 238
fprintf(stderr, "ERROR: unknown option '%s'\n", argv[arg]);
238 239
err++;
@@ -268,6 +269,8 @@ main(int argc, char **argv) {
268 269
fprintf(stderr, " -eE erate maximum error rate of evidence overlaps\n");
269 270
fprintf(stderr, " -eC coverage maximum coverage of evidence reads to emit\n");
270 271
fprintf(stderr, "\n");
272 +
fprintf(stderr, " -xC coverage estimated coverage in input reads\n");
273 +
fprintf(stderr, "\n");
271 274 272 275
if (seqName == NULL)
273 276
fprintf(stderr, "ERROR: no input seqStore (-S) supplied.\n");
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