[med-svn] samtools annotated tag 0.1.13 created (now eb3e61c)

[Charles Plessy]

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plessy pushed a change to annotated tag 0.1.13
in repository samtools.

        at  eb3e61c   (tag)
   tagging  727b8c146c0146f6c43b2a7ab75c4c7bc3f91eef (commit)
  replaces  0.1.12a
 tagged by  On behalf of Heng Li
        on  Tue Mar 1 19:58:23 2011 +0000

- Log -----------------------------------------------------------------
Samtools 0.1.13, including ChangeLog.old and win32/lib*.a files
that were missing from the canonical release tarball.

Heng Li (42):
      more informative error message
      * remove "-f". Instead always compute consensus quality
      vcf->fastq
      Fixed a compiling error when knetfile is not used.
      bring back the windows support
      In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
      added a warning for the Windows version
      fixed a bug in vcf2fq
      * samtools-0.1.12-1 (r873)
      a spelling error..
      * samtools-0.1.12-2 (r877)
      Make sure that the GT genotype field is the first
      * fixed a minor issue in printing VCFs
      drop bcf-fix.pl as it is redundant by the latest changes
      compute max SP and max GQ from sample genotypes
      * samtools-0.1.12-4 (r884)
      (Arguably) improved the indel caller a tiny bit for lowCov data.
      * samtools-0.1.12-6 (r887)
      When -B is applied to mpileup, still use paired reads only unless -A is flagged.
      * samtools-0.1.12-12 (r889)
      * samtools-0.1.12-9 (r891)
      added ST
      sorry. It is SP not ST
      * samtools-0.1.12-10 (r896)
      move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
      fixed two minor bugs in Fisher's exact test
      * fixed a rare memory issue in bam_md.c
      * avoid a segfault when network connect fails
      * fixed an out-of-boundary bug
      fixed a typo in the VCF header
      finished VCF->BCF conversion
      * automatically fix errors in GL
      more meaningful BAM truncation message
      added "const" to bcf_p1_cal()
      added the phase command
      update the BCF spec
      * change the order of PL/GL according to the latest VCF spec
      * put version number in bam.h
      * 0.1.12-r924:126
      minor changes to a heuristic rule
      * optionally drop phase ambiguous reads
      Release samtools-0.1.13 (r926:134)

On behalf of John Marshall (1):
      System libraries go *after* user libraries in link commands, because

Petr Danecek (4):
      Fixed the VCF header to pass validation
      Fixed a typo in read_samples
      Skip sites with unknown ref
      Prevent division by zero

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No new revisions were added by this update.

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