Change output format to show Genotype rather than Alt Base #19
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There was an assumption that there would not be greater than 15 different characters used in a given position between sequences. This is unlikely to be possible in well formatted files but it could be the case in an input file is corrupted.
GT format reports the index into a list of alleles rather than the relevant allele
The previous behaviour output an Alt Base which was not understood by some other tools. This changes the format to GT.
bewt85
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@satta, if you have a minute, would you mind reviewing this for me? |
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closed while I make changes discussed with @satta |
Use calloc and strlen to simplify the vcf related code
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@satta I've made most of the changes we discussed. I've not removed the |
satta
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Jul 16, 2015
Change output format to show Genotype rather than Alt Base
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Part of ticket 471874
Previously snp_sites reported the value of the alternate base if present else returned '.' if the base matched the reference sequence. Unfortunately some tools (like Plink and PyVCF) did not understand this format. I've therefore implemented the suggested Genotype format in the spec.
This is a breaking change so I've bumped the VERSION to 2.0.0