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==== Specifying Discard Rules ====
==== Specifying Discard Rules ====
===== Basic Rules =====
When specifying the discard rules, you should use the constants found at the top of VcfFileReader.h
When specifying the discard rules, you should use the constants found at the top of VcfFileReader.h
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and discards reads that do not have <code>PASS</code> in the <code>FILTER</code> field and reads that have a genotype that is not phased or have no <code>GT</code> in the <code>FORMAT</code> fields.
and discards reads that do not have <code>PASS</code> in the <code>FILTER</code> field and reads that have a genotype that is not phased or have no <code>GT</code> in the <code>FORMAT</code> fields.
===== Additional Rules =====
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">
VcfFileReader::addDiscardMinAltAlleleCount(int32_t minAltAlleleCount, VcfSubsetSamples* subset)
</source>
The <code>VcfSubsetSamples* subset</code> parameter is a pointer to the subset of samples that you want to include when counting the number of alternate alleles. If all samples that are read/kept are to be included, NULL should be passed in.
The <code>minAltAlleleCount</code> parameter is the minimum number of alternate alleles found in the subset in order for the record to be kept.
==== Read only Certain Sections of the File / Using a VCF Index (TABIX) File ====
==== Read only Certain Sections of the File / Using a VCF Index (TABIX) File ====
