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LibStatGen: VCF

1,476 bytes added, 16:34, 25 July 2012
Minimum Alternate Allele Count
===== Minimum Alternate Allele Count =====
There are additional discard rules that can be specified by calling methods on VcfFileReader.
 
To Discard any records without a minimum number of alternate alleles, use:
<source lang="cpp">
<source lang="cpp">
VcfFileReader::rmDiscardMinAltAlleleCount()
</source>
 
===== Minimum Minor Allele Count =====
To Discard any records without a minimum number of minor alleles, use:
<source lang="cpp">
VcfFileReader::addDiscardMinMinorAlleleCount(int32_t minMinorAlleleCount, VcfSubsetSamples* subset)
</source>
 
The <code>minMinorAlleleCount</code> parameter is the minimum number of minor alleles found in the specified subset (if specified) in order for the record to be kept.
 
The <code>VcfSubsetSamples* subset</code> parameter is a pointer to the subset of samples that you want to include when counting the number of alleles. If all samples that are read/kept are to be included, NULL should be passed in.
 
To specify a <code>VcfSubsetSamples</code> use the constructor:
<source lang="cpp">
void VcfSubsetSamples::init(const VcfHeader& header, bool include)
</source>
Pass in the header that was read from the VCF file. Set <code>include</code> to true if all samples should be included except any that are specified as excluded. Set <code>include</code> to false if all samples should be excluded except any that are specified as included. NOTE: the header is not modified to add/remove any samples.
 
To mark a specific sample as excluded use:
<source lang ="cpp">
bool VcfSubsetSamples::addExcludeSample(const char* sampleName);
</source>
To mark a specific sample as included use:
<source lang ="cpp">
bool VcfSubsetSamples::addIncludeSample(const char* sampleName);
</source>
 
Use the following method to remove the DiscardMinMinorAlleleCount rule:
<source lang="cpp">
VcfFileReader::rmDiscardMinMinorAlleleCount()
</source>

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