Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

VCFv4.3 - first batch of changes #88

Merged
merged 35 commits into from
Oct 10, 2015
Merged

VCFv4.3 - first batch of changes #88

merged 35 commits into from
Oct 10, 2015

Commits on Jul 28, 2014

  1. Added VCFv4.3 draft, changes marked in red color

    @pd3
    pd3 committed Jul 28, 2014
    Configuration menu
    Copy the full SHA
    af41ed9 View commit details
    Browse the repository at this point in the history

Commits on Aug 1, 2014

  1. Adding subsection about gVCF files.

    Ryan Poplin committed Aug 1, 2014
    Configuration menu
    Copy the full SHA
    2d3f041 View commit details
    Browse the repository at this point in the history

Commits on Aug 11, 2014

  1. Updated gVCF section, added list of changes

    @pd3
    pd3 committed Aug 11, 2014
    Configuration menu
    Copy the full SHA
    4ca3424 View commit details
    Browse the repository at this point in the history

Commits on Sep 8, 2014

  1. Added a gVCF section plus minor edits

    @pd3
    pd3 committed Sep 8, 2014
    Configuration menu
    Copy the full SHA
    efed15f View commit details
    Browse the repository at this point in the history

Commits on Sep 19, 2014

  1. Forbid duplicate fields, UTF8 the only encoding.

    @pd3
    pd3 committed Sep 19, 2014
    Configuration menu
    Copy the full SHA
    a09e56f View commit details
    Browse the repository at this point in the history

Commits on Sep 23, 2014

  1. Removed forgotten copy and paste error, resolves #41

    @pd3
    pd3 committed Sep 23, 2014
    Configuration menu
    Copy the full SHA
    af36fb1 View commit details
    Browse the repository at this point in the history

  2. Introduced symbolic allele "<*>" in gVCF

    @pd3
    pd3 committed Sep 23, 2014
    Configuration menu
    Copy the full SHA
    4a91745 View commit details
    Browse the repository at this point in the history

Commits on Oct 1, 2014

  1. Add ##META definitions

    @pd3
    pd3 committed Oct 1, 2014
    Configuration menu
    Copy the full SHA
    7789a1b View commit details
    Browse the repository at this point in the history

Commits on Oct 2, 2014

  1. Include META header lines in the list of changes

    @pd3
    pd3 committed Oct 2, 2014
    Configuration menu
    Copy the full SHA
    250a88c View commit details
    Browse the repository at this point in the history

Commits on Oct 15, 2014

  1. Clarification: no negative values in GT array except the end-of-vecto… 

    …r byte
    @pd3
    pd3 committed Oct 15, 2014
    Configuration menu
    Copy the full SHA
    1080e8a View commit details
    Browse the repository at this point in the history

Commits on Jan 5, 2015

  1. Clarified GL ordering. Resolves #58

    @pd3
    pd3 committed Jan 5, 2015
    1 Configuration menu
    Copy the full SHA
    66d45d5 View commit details
    Browse the repository at this point in the history

Commits on Jan 26, 2015

  1. Merge branch 'master' into VCFv4.3

    @pd3
    pd3 committed Jan 26, 2015
    Configuration menu
    Copy the full SHA
    ce805dd View commit details
    Browse the repository at this point in the history

Commits on Apr 30, 2015

  1. Fix #82

    @pd3
    pd3 committed Apr 30, 2015
    Configuration menu
    Copy the full SHA
    aabe553 View commit details
    Browse the repository at this point in the history

  2. Fix #82

    @pd3
    pd3 committed Apr 30, 2015
    Configuration menu
    Copy the full SHA
    61d0f01 View commit details
    Browse the repository at this point in the history

Commits on May 19, 2015

  1. Fix SVLEN example, resolves #84

    @pd3
    pd3 committed May 19, 2015
    Configuration menu
    Copy the full SHA
    672b512 View commit details
    Browse the repository at this point in the history

  2. Fix SVLEN examplein VCFv4.3, resolves #84

    @pd3
    pd3 committed May 19, 2015
    Configuration menu
    Copy the full SHA
    73482c0 View commit details
    Browse the repository at this point in the history

  3. Update minor version number, resolves #63

    @pd3
    pd3 committed May 19, 2015
    Configuration menu
    Copy the full SHA
    8f6b7cf View commit details
    Browse the repository at this point in the history

Commits on Jun 2, 2015

  1. List of changes: 

    - meta-information lines must be key=value pairs (#67)
- an ID attribute is required in structured header lines, unique within its type
- the above point newly requires ID in the reserved PEDIGREE tag
- new reserved AD, ADF, and ADR FORMAT and INFO fields added, resolves #78
- reorder list of INFO and FORMAT tags alphabetically
- removed UNICODE-characters-not-supported sentence from BCF specification, in partial response to #65
    @pd3
    pd3 committed Jun 2, 2015
    Configuration menu
    Copy the full SHA
    f247cee View commit details
    Browse the repository at this point in the history

Commits on Jun 3, 2015

  1. GL ordering made clearer as discussed in #83

    @pd3
    pd3 committed Jun 3, 2015
    Configuration menu
    Copy the full SHA
    d6b46df View commit details
    Browse the repository at this point in the history

Commits on Jun 11, 2015

  1. Be definitive in the ##fileformat section 

    This section specifies ##fileformat, not just gives an example.
    @jmarshall
    jmarshall committed Jun 11, 2015
    Configuration menu
    Copy the full SHA
    08506d8 View commit details
    Browse the repository at this point in the history

Commits on Jun 22, 2015

  1. Removed ill-defined GLE tag, resolves #90

    @pd3
    pd3 committed Jun 22, 2015
    Configuration menu
    Copy the full SHA
    1c5e278 View commit details
    Browse the repository at this point in the history

  2. Data Types section, describe valid float format, NaN and +/-Inf are a… 

    …llowed
    @pd3
    pd3 committed Jun 22, 2015
    Configuration menu
    Copy the full SHA
    db372bc View commit details
    Browse the repository at this point in the history

Commits on Jun 29, 2015

  1. Extended bits about character encoding 

    - added list of non-printable characters
- specified the percent encoding
- lines should not end with TAB
- last line in the file should end with new line separator
    @pd3
    pd3 committed Jun 29, 2015
    Configuration menu
    Copy the full SHA
    c128680 View commit details
    Browse the repository at this point in the history

  2. Chromosome names cannot use reserved symbolic alleles and contain cha… 

    …racters used by breakpoints
    @pd3
    pd3 committed Jun 29, 2015
    Configuration menu
    Copy the full SHA
    c50589b View commit details
    Browse the repository at this point in the history

  3. Reference SV INFO and FORMAT section from the main text

    @pd3
    pd3 committed Jun 29, 2015
    Configuration menu
    Copy the full SHA
    4f49af0 View commit details
    Browse the repository at this point in the history

  4. IUPAC ambiguity codes, as per #54

    @pd3
    pd3 committed Jun 29, 2015
    Configuration menu
    Copy the full SHA
    6cc5604 View commit details
    Browse the repository at this point in the history

Commits on Jun 30, 2015

  1. Fixed the wording of trailing tabs and IUPAC codes from "should" to "… 

    …must"
    @pd3
    pd3 committed Jun 30, 2015
    Configuration menu
    Copy the full SHA
    4b381fa View commit details
    Browse the repository at this point in the history

Commits on Jul 22, 2015

  1. Remove repeated text about INFO fields for imprecise structural varia… 

    …nts. Insert missing 'of' into sentence about precise variants consensus sequence
    @bjpop @pd3
    bjpop authored and pd3 committed Jul 22, 2015
    Configuration menu
    Copy the full SHA
    31bd4cc View commit details
    Browse the repository at this point in the history

Commits on Jul 29, 2015

  1. PEDIGREE VCF header lines now require ID tag, resolves #96 

    Plus minor change of wording in ALT * description, "overlapping" rather
than "upstream" deletion.
    @pd3
    pd3 committed Jul 29, 2015
    Configuration menu
    Copy the full SHA
    51b4cb6 View commit details
    Browse the repository at this point in the history

Commits on Aug 24, 2015

  1. Clarifications made as requested by #88 (comment)

    @pd3
    pd3 committed Aug 24, 2015
    Configuration menu
    Copy the full SHA
    56e8bae View commit details
    Browse the repository at this point in the history

Commits on Sep 9, 2015

  1. Fix inconsistent description of PASS in BCF. 

    The implicit filter PASS was described inconsistently throughout BCFv2.1.
It is encoded as the first entry in the dictionary, not the last.
    @pd3
    pd3 committed Sep 9, 2015
    Configuration menu
    Copy the full SHA
    187745f View commit details
    Browse the repository at this point in the history

Commits on Sep 24, 2015

  1. Removed red coloring from the text, VCFv4.3 is ready to be merged

    @pd3
    pd3 committed Sep 24, 2015
    Configuration menu
    Copy the full SHA
    d3a28e2 View commit details
    Browse the repository at this point in the history

Commits on Oct 10, 2015

  1. Modified example, coordinates must be ordered

    @pd3
    pd3 committed Oct 10, 2015
    Configuration menu
    Copy the full SHA
    861e235 View commit details
    Browse the repository at this point in the history

  2. Move sentences which apply to all data lines from 1.6.1 to 1.6

    @pd3
    pd3 committed Oct 10, 2015
    Configuration menu
    Copy the full SHA
    ad14194 View commit details
    Browse the repository at this point in the history

  3. Stronger wording about disallowed INT32 values

    @pd3
    pd3 committed Oct 10, 2015
    Configuration menu
    Copy the full SHA
    fe0222c View commit details
    Browse the repository at this point in the history