* added a switch to allow anomalous read pairs in calling
int c;
const char *file_list = NULL;
char **fn = NULL;
int c;
const char *file_list = NULL;
char **fn = NULL;
+ int nfiles = 0, use_orphan = 0;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
mplp.max_mq = 60;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
mplp.max_mq = 60;
mplp.max_depth = 250;
mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
mplp.max_depth = 250;
mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
- while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:P:o:e:h:I")) >= 0) {
+ while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:b:P:o:e:h:I")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
- case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
case 'R': mplp.flag |= MPLP_REALN; break;
case 'D': mplp.flag |= MPLP_FMT_DP; break;
case 'S': mplp.flag |= MPLP_FMT_SP; break;
case 'R': mplp.flag |= MPLP_REALN; break;
case 'D': mplp.flag |= MPLP_FMT_DP; break;
case 'S': mplp.flag |= MPLP_FMT_SP; break;
case 'o': mplp.openQ = atoi(optarg); break;
case 'e': mplp.extQ = atoi(optarg); break;
case 'h': mplp.tandemQ = atoi(optarg); break;
case 'o': mplp.openQ = atoi(optarg); break;
case 'e': mplp.extQ = atoi(optarg); break;
case 'h': mplp.tandemQ = atoi(optarg); break;
+ case 'A': use_orphan = 1; break;
+ if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
if (argc == 1) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
if (argc == 1) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
fprintf(stderr, " -h INT coefficient for homopolyer errors [%d]\n", mplp.tandemQ);
fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
fprintf(stderr, " -h INT coefficient for homopolyer errors [%d]\n", mplp.tandemQ);
+ fprintf(stderr, " -A use anomolous read pairs in SNP/INDEL calling\n");
fprintf(stderr, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
fprintf(stderr, " -B disable BAQ computation\n");
fprintf(stderr, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
fprintf(stderr, " -B disable BAQ computation\n");
#endif
#ifndef PACKAGE_VERSION
#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.12a (r862)"
+#define PACKAGE_VERSION "0.1.12-1 (r873)"
#endif
int bam_taf2baf(int argc, char *argv[]);
#endif
int bam_taf2baf(int argc, char *argv[]);