[med-svn] samtools annotated tag 0.1.8 created (now 75b4d91)

[Charles Plessy]

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plessy pushed a change to annotated tag 0.1.8
in repository samtools.

        at  75b4d91   (tag)
   tagging  aecbff7298d7df0ac206fc5c45aa91d758c1b502 (commit)
  replaces  0.1.7a
 tagged by  On behalf of Heng Li
        on  Mon Jul 12 03:47:20 2010 +0100

- Log -----------------------------------------------------------------
Samtools 0.1.8, including ChangeLog.old and win32/lib*.a files
that were missing from the canonical release tarball, but without
the samtools.txt file (generated from samtools.1) that is found
in the tarball.

Heng Li (36):
      * samtools-0.1.7-1 (r515)
      another example program
      * samtools-0.1.7-2 (r520)
      * samtools-0.1.7-3 (r521)
      * samtools-0.1.7-4 (r522)
      * samtools-0.1.7-5 (r528)
      * samtools-0.1.7-6
      added a hidden option in pileup to output the base position (for Erin)
      Updated export2sam.pl by Chris Saunders from Illumina.
      * samtools-0.1.7-7 (r584)
      * samtools-0.1.7-8 (r585)
      * samtools-0.1.7-9 (r586)
      * samtools-0.1.7-10 (r587)
      * samtools-0.1.7-11 (r588)
      * samtools-0.1.7-12 (r589)
      * samtools-0.1.7-13 (r590)
      * samtools-0.1.7-14 (r591)
      * samtools-0.1.7-15 (r592)
      rename iterf as iter
      fixed a bug for unmapped sequences in indexing
      * samtools-0.1.7-16 (r595)
      * samtools-0.1.7-17 (r596)
      added Makefile targets to compile shared/dynamic library
      minor fix. No actual effect.
      change printf() to puts in exporting
      fixed a minor bug in indexing
      fixed a minor bug in idxstats
      * samtools-.1.7-18 (r605)
      removed a debugging example
      * samtools-0.1.7-r607
      * make tview more friendly
      make pileup work with CIGAR with I/D at the beginning or in the end
      change the command line option of pileup
      fixed a bug in sorting when output to stdout (by Peter Chines)
      fixed a compiling issue for Windows
      Release samtools-0.1.8

On behalf of John Marshall (8):
      Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
      Index files should be opened in binary mode, not text mode.
      Also clean *.exe (for Cygwin users using this makefile).
      Put libraries at the end, so they can resolve references from libbam.a
      Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
      Depend on libbam.a rather than the phony target, so that samtools is not
      Put the right filename in the error message.
      Improve the invalid 'BAM\1' magic number error message, and also print it

Petr Danecek (16):
      Allow tabs in the CO header field
      Small fix in VCF format: dot for the empty INFO field
      Fixed a bug in knet_seek
      Added VCF header
      Added the -d option to limit maximum depth for indels.
      Added possibility to specify a custom column title for the data column
      Print an error for pileups in simple format
      Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
      Improved efficiency of header parsing
      Added possibility to select indels only and fixed a bug in reporting homozygous indels.
      Fixed the order of sequences in the header
      Speedup with -i, no need to query the reference all the time
      More descriptive message for space separated tags
      Added the possibility to print or not to print the reference allele
      Added a note about the indels coordinates
      Initial release on behalf of Aylwyn Scally

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No new revisions were added by this update.

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