[med-svn] [htslib] annotated tag 0.2.0-rc6 created (now 3479607)

[Charles Plessy]

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plessy pushed a change to annotated tag 0.2.0-rc6
in repository htslib.

        at  3479607   (tag)
   tagging  0e76a594c47f5808b7ee483664245e1144bc3c46 (commit)
  replaces  0.2.0-rc5
 tagged by  John Marshall
        on  Thu Feb 13 17:30:59 2014 +0000

- Log -----------------------------------------------------------------
Test release RC6

James Bonfield (16):
      Cope with empty containers internal to a CRAM stream.
      Added implementation of cram_external_encode(). It's not yet used
      Bug fix to the zlib strategy tuning in multi-threaded mode. It could
      Added refs_t->last_id (note distinct from ->last) for use when reading
      Add mfsteal to mFILE, and use it in cram_populate_ref.
      Added missing return code checks.  Fixed 'x' mode of mfreopen.
      Added some EOF block creation and checking.
      Bug fix to cram_next_slice().  The new while loop checking for
      Bug fix to EOF block writing when in multi-threaded mode (not yet
      Added a check to EOF in Cram in hts_close(). Note that this isn't the
      Merge branch 'develop' of https://github.com/samtools/htslib into develop
      Updated the Cram EOF block detection to avoid falsely considering the
      Merge branch 'develop' of https://github.com/samtools/htslib into develop
      Fixed initialisation of CRAM indexing when the CRAM file contains
      Initialise beg and end values in the hts iterator. Without these
      Fixed the iterator to be 1-based inclusive coordinates for CRAM.

John Marshall (10):
      Fix hseek() return value test
      Make filename argument a *const* char pointer
      Store readrec function pointer within hts_itr_t
      Make search key arguments *const* char pointers
      Write strcmp() comparisons comprehensibly
      Add basic test exercising bcf_itr_queryi and bcf_itr_querys
      hts_itr_querys() calls hts_itr_query() via a function parameter
      Add sam_itr_*() dealing with BAM and CRAM iterators interchangeably
      Also initialise tid in case user code looks at it
      Merge pull request #46, CRAM EOF blocks

Petr Danecek (38):
      Merge branch 'develop' into bcftools+calling
      sam: New bam_str2flag and bam_flag2str functions for a more user-friendly setting of bitmasks. Removed the default pileup filters (except for BAM_FUNMAP) and moved the filtering to BAM-reading callbacks
      Merge branch 'bcftools+calling' into develop
      Merge branch 'develop' into bcftools+calling
      Merge branch 'bcftools+calling' into develop
      faidx: Detect compressed BGZF fasta files and create .gzi index without asking to allow proper functioning of samtools faidx fasta.fa.gz
      synced_reader: Improved regions/targets to be faster with large number of sequences; More userfriendly regions_overlap() function
      vcf: bcf_update_format now sets the number of samples in VCF record which previously was responsibility of the user; Fix in bcf_itr_querys macro, non-existent bcf_name2id renamed to bcf_hdr_name2id
      vcf: Support for IDX BCF tag
      vcf: Output . for missing INFO, FMT and samples
      vcf.c: Fixed a renaming artifact, bcf_clear1 should be bcf_clear
      vcf: qual now set to missing on bcf_clear; Avoid warnings about type-punned pointers
      Output VCFv4.2 header
      Merge branch 'develop' into bcftools+calling
      Updated test
      vcf: Make sure fileformat is added only once
      vcf: New bcf_get_info_string() wrapper
      vcf: New API bcf_get_format_string()
      Allow overriding default columns indexes in bcf_sr_regions_init
      vcf: new function bcf_remove_filter()
      Merge branch 'develop' into bcftools+calling
      Merge branch 'bcftools+calling' into develop
      vcf: fix in bcf_get_genotypes, sanity check too strict for GT
      vcf: Tip to workaround missing contig tags
      hts indexing: Allow arbitrary chromosomal order.
      vcf: New bcf_hdr_id2hrec() and bcf_hrec_format() functions
      vcf: New vcf_write_line() function
      synced_bcf_reader: New bcf_sr_seek() function
      vcf: New bcf_translate() and bcf_hdr_combine() API
      idx: Support for "." queries to retrieve all records
      vcf: New bcf_has_filter() API function
      vcf: new experimental bcf_hdr_set_samples() for subsetting
      Strict matching of strings in bam_str2flag
      Merge branch 'bcftools+calling' into develop
      bcf_hdr_set_samples() recognise lists vs file names
      synced_reader: Better handling of target alleles
      bcf_sr_set_samples to use the new --sample convention
      vcf: New bcf_get_info_flag() API

Shane McCarthy (3):
      add support for Number=R fields when trimming alleles
      Merge branch 'develop' of git://github.com/samtools/htslib into feature/number_R
      add support for Number=R fields when trimming alleles

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