<code>VcfFileReader</code> is declared in <code>VcfFileReader.h</code>, so be sure to include that file.
Subsetting Samples ====
To select only a subset of samples to keep, when opening the file also specify the name of the file containing the names of the samples to keep and the delimiter separating the sample names (default is a new line, '\n').
===== 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:
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.
To specify a <code>VcfSubsetSamples</code> use the constructor:
void VcfSubsetSamples:: init( const VcfHeader& header, bool include)
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) ;
Use the following method to remove the
==== Read only Certain Sections of the File / Using a VCF Index (TABIX) File ====
** <code>allPhased()</code> returns true if all the samples are phased and none unphased and false if any are not phased
** <code>allUnphased()</code> returns true if all the samples are unphased and none phased and false if any are not unphased
** <code>hasAllGenotypeAlleles()</code> returns true if all the samples have all the genotype alleles specified and false if any are missing or the GT field is missing.
=== VcfRecordFilter ===
<code>VcfRecords</code> contain the data from the <code>INFO</code> field in a <code>VcfRecordFilter</code> object.