+14
-2
lines changedFilter options
+14
-2
lines changed Original file line number Diff line number Diff line change
@@ -28,6 +28,7 @@ int
28 28
main(int argc, char **argv) {
29 29
char *outName = NULL;
30 30
char *seqName = NULL;
31 +
int32 minLength = 0;
31 32 32 33
vector<char *> files;
33 34
@@ -41,6 +42,9 @@ main(int argc, char **argv) {
41 42
} else if (strcmp(argv[arg], "-S") == 0) {
42 43
seqName = argv[++arg];
43 44 45 +
} else if (strcmp(argv[arg], "-minlength") == 0) {
46 +
minLength = strtoint32(argv[++arg]);
47 + 44 48
} else if (fileExists(argv[arg])) {
45 49
files.push_back(argv[arg]);
46 50
@@ -55,6 +59,7 @@ main(int argc, char **argv) {
55 59
if ((err) || (seqName == NULL) || (outName == NULL) || (files.size() == 0)) {
56 60
fprintf(stderr, "usage: %s -S seqStore -o output.ovb input.mhap[.gz]\n", argv[0]);
57 61
fprintf(stderr, " Converts mhap native output to ovb\n");
62 +
fprintf(stderr, " -minlength X discards overlaps below X bp long.\n");
58 63 59 64
if (seqName == NULL)
60 65
fprintf(stderr, "ERROR: no seqStore (-S) supplied\n");
@@ -147,9 +152,16 @@ main(int argc, char **argv) {
147 152
ov.dat.ovl.bhg5, ov.dat.ovl.bhg3,
148 153
(ov.dat.ovl.flipped) ? " flipped" : ""), exit(1);
149 154 150 -
// Overlap looks good, write it!
155 +
// Overlap looks good, write it if its long enough. Bogart is
156 +
// computing overlap length as the max number of bases covered on
157 +
// either read.
158 + 159 +
int32 oalen = alen - ov.dat.ovl.ahg5 - ov.dat.ovl.ahg3;
160 +
int32 oblen = blen - ov.dat.ovl.bhg5 - ov.dat.ovl.bhg3;
151 161 152 -
of->writeOverlap(&ov);
162 +
if ((minLength <= oalen) ||
163 +
(minLength <= oblen))
164 +
of->writeOverlap(&ov);
153 165
}
154 166 155 167
delete in;
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