This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository samtools.
commit 92a1cb3d57e0689e051931407037d45462f46b20 Merge: d0ebd20 4ce9296 Author: John Marshall <[email protected]> Date: Fri Nov 22 17:15:36 2013 +0000 Merge branch master of git://github.com/leecbaker/samtools Some of the files in the original PR have moved to the bcftools repository, and the remaining type mismatches of this kind have been fixed there. bam2bcf_indel.c | 2 +- bam2depth.c | 4 ++-- bam_lpileup.c | 2 +- bam_plcmd.c | 8 ++++---- bam_sort.c | 4 ++-- bamshuf.c | 4 ++-- bedcov.c | 6 +++--- kprobaln.c | 4 ++-- phase.c | 8 ++++---- sam_header.c | 2 +- sample.c | 2 +- 11 files changed, 23 insertions(+), 23 deletions(-) diff --cc bam_plcmd.c index 74034f1,ee4a151..eb56253 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@@ -254,22 -203,16 +254,22 @@@ static int mpileup(mplp_conf_t *conf, i memset(&gplp, 0, sizeof(mplp_pileup_t)); memset(&buf, 0, sizeof(kstring_t)); memset(&bc, 0, sizeof(bcf_call_t)); - data = calloc(n, sizeof(void*)); - plp = calloc(n, sizeof(void*)); - n_plp = calloc(n, sizeof(int*)); + data = calloc(n, sizeof(mplp_aux_t*)); + plp = calloc(n, sizeof(bam_pileup1_t*)); + n_plp = calloc(n, sizeof(int)); sm = bam_smpl_init(); - // read the header and initialize data + if (n == 0) { + fprintf(stderr,"[%s] no input file/data given\n", __func__); + exit(1); + } + + // read the header of each file in the list and initialize data for (i = 0; i < n; ++i) { - bam_header_t *h_tmp; + bam_hdr_t *h_tmp; data[i] = calloc(1, sizeof(mplp_aux_t)); - data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r"); + data[i]->fp = sam_open(fn[i], "rb"); + hts_set_fai_filename(data[i]->fp, conf->fai_fname); if ( !data[i]->fp ) { fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno)); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
