Correctly format contig output lines from writer, making output VCFs compatible with GATK. Fixes #74 #81

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This is a fix for issue 74:

#74

The raw dictionary output of PyVCF on contig lines causes errors if you process files downstream with GATK. This pull request detects and correctly formats "##contig" metadata. Includes an added test case to avoid regression.

jamescasbon pushed a commit that referenced this pull request Jan 2, 2013

James Casbon
Merge pull request #81 from chapmanb/master
Correctly format contig output lines from writer, making output VCFs compatible with GATK. Fixes #74

@jamescasbon jamescasbon merged commit 9ca7798 into jamescasbon:master Jan 2, 2013

martijnvermaat added a commit to martijnvermaat/PyVCF that referenced this pull request Jan 10, 2013

Correctly write meta lines with dictionary value
Write meta lines with a dictionary-like value as

    ##meta=<field=value,field=value,...>

instead of as the Python dictionary string representation. This is a
fix for jamescasbon#83 and a generalization of jamescasbon#81. A
regression compared to jamescasbon#81 is that the order of fields in
a `contig` line is no longer defined.

gotgenes pushed a commit to gotgenes/PyVCF that referenced this pull request May 13, 2014

James Casbon
Merge pull request #81 from chapmanb/master
Correctly format contig output lines from writer, making output VCFs compatible with GATK. Fixes #74

gotgenes pushed a commit to gotgenes/PyVCF that referenced this pull request May 13, 2014

Correctly write meta lines with dictionary value
Write meta lines with a dictionary-like value as

    ##meta=<field=value,field=value,...>

instead of as the Python dictionary string representation. This is a
fix for jamescasbon#83 and a generalization of jamescasbon#81. A
regression compared to jamescasbon#81 is that the order of fields in
a `contig` line is no longer defined.
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