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Commits on Nov 7, 2014

• Fix compilation when ALLOW_UAC is not defined

  jmarshall

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• Merge pull request samtools#142 from reinders/patch-1

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  pd3

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Commits on Nov 6, 2014

• Buffer overflow error in synced_bcf_reader.c

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  reinders

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  4aa494f

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• Fix of memmove bug in bcf_remove_filter()

  pd3

  committed
  4d13ff0

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• Fixed an incorrect EOF-style case when seeking multiple times.

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  jkbonfield

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• Sped up cram_index_load some 200 fold by replacing sscanf with our own

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  jkbonfield

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Commits on Nov 3, 2014

• Parse SAM aux 'i' values > 2^31 correctly

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  jmarshall

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• Merge origin/develop, replacing htsFile.type by .format

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  jmarshall

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Commits on Oct 30, 2014

• tbx: Detect faulty tbi files

  pd3

  committed
  244dde8

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• Reverting 9e844e0 and rewriting in a

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  jkbonfield

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Commits on Oct 29, 2014

• Fixed an error found via valgrind of test_view -D c1#pad1.tmp.cram.

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  jkbonfield

  committed
  7a13d83

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• Fix bug spotted by valgrind when running "./test_view -D

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  jkbonfield

  committed
  9e844e0

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• Fix a bug where hts_set_fai_filename() didn't pass this through to

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  jkbonfield

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  a98d88f

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• In a bid to keep the DEBUG_printf line potentially printing up the

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  jkbonfield

  committed
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• bcf_translate: Be aware of gaps in BCF headers

  pd3

  committed
  9c510fb

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• Fix in bgzf's gzip reading plus added a test for this

  pd3

  committed
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Commits on Oct 27, 2014

• Amended the compression level checking code in cram_dopen() to follow

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  jkbonfield

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Commits on Oct 22, 2014

• Add htsfile utility

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  jmarshall

  committed
  41ab01b

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• Use htsFormat to replace htsFile's is_foo flags

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  jmarshall

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Commits on Oct 21, 2014

• Do not load remote index if already exists locally

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  pd3

  committed
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• Do not use 0x80 & co for missing alleles

  pd3

  committed
  eda497b

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• Clean up, is_compressed and is_cram no longer necessary

  pd3

  committed
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Commits on Oct 20, 2014

• Removed old hts_file_type() API and replaced it with the new htsFormat;

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  pd3

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Commits on Oct 17, 2014

• Add htsFormat and format-detection API functions

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  jmarshall

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Commits on Oct 16, 2014

• Merge CRAM v3 updates (PR samtools#132)

  jmarshall

  committed
  233e159

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• Fix cram/rANS_* dependencies

  jmarshall

  committed
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• Remove -DSAMTOOLS vestiges

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  jmarshall

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• Added copyright notice.

  jkbonfield

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Commits on Oct 15, 2014

• Split off the rans_byte.h portion of rANS_static.c back into its own

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  jkbonfield

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Commits on Oct 14, 2014

• New bcf_copy API

  pd3

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Commits on Oct 10, 2014

• VCF header editing speedup for large number of ref sequences

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  pd3

  committed
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Commits on Oct 6, 2014

• Support for Type=Character, in htslib same as Type=String

  pd3

  committed
  912a7d0

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• Merge man page formatting fixes

  jmarshall

  committed
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Commits on Oct 3, 2014

• Fix regidx.o dependencies and htslib.mk; alphabetise

  jmarshall

  committed
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• regidx: use size_t, not ssize_t

  pd3

  committed
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