From 6ed91e9cf6d11c718bc8b2bea412108555d55bba Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 8 Dec 2010 03:39:57 +0000 Subject: [PATCH] * samtools-0.1.12-1 (r873) * added a switch to allow anomalous read pairs in calling --- bam_plcmd.c | 8 +++++--- bamtk.c | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/bam_plcmd.c b/bam_plcmd.c index 002297a..29fbb9c 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -850,7 +850,7 @@ int bam_mpileup(int argc, char *argv[]) int c; const char *file_list = NULL; char **fn = NULL; - int nfiles = 0; + int nfiles = 0, use_orphan = 0; mplp_conf_t mplp; memset(&mplp, 0, sizeof(mplp_conf_t)); mplp.max_mq = 60; @@ -859,7 +859,7 @@ int bam_mpileup(int argc, char *argv[]) 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); @@ -873,7 +873,6 @@ int bam_mpileup(int argc, char *argv[]) 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; @@ -886,8 +885,10 @@ int bam_mpileup(int argc, char *argv[]) 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"); @@ -903,6 +904,7 @@ int bam_mpileup(int argc, char *argv[]) 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"); diff --git a/bamtk.c b/bamtk.c index 8d8a8dd..a5a0da3 100644 --- a/bamtk.c +++ b/bamtk.c @@ -9,7 +9,7 @@ #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[]); -- 2.39.2