[med-svn] samtools 04/26: Merge branch master of git://github.com/leecbaker/samtools

[Charles Plessy]

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plessy pushed a commit to branch debian/unstable
in repository samtools.

commit 92a1cb3d57e0689e051931407037d45462f46b20
Merge: d0ebd20 4ce9296
Author: John Marshall <jm18 at sanger.ac.uk>
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));

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