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LibStatGen: VCF

2,002 bytes added, 09:55, 29 March 2012
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Once you have the record, use methods from the <code>VcfRecord</code> to extract the desired information.
 
==== Extracting Data from the Record ====
Do not delete any of the returned pointers. They are references to strings within the record and will not be valid when the record changes or is deleted.
 
* Position Information
** <code>getChromStr()</code> returns const char* to this record's chromosome string
** <code>get1BasedPosition()</code> returns an integer containing the 1-based position of the record
* Identifiers
** <code>getIDStr()</code> returns const char* to this record's ID. It includes the entire list of unique identifiers delimited by ';'
* Information on Bases
** <code>getRefStr()</code> returns const char* to the entire reference string
** <code>getAltStr()</code> returns const char* to the entire alternate string (alternates seperated by ',')
** <code>getNumAlts()</code> returns an integer containing the number of alternates in the alt string.
* Quality Information
** <code>getQual()</code> returns a float containing the phred quality score
** <code>getQualStr()</code> returns a string containing the phred quality score
* Filter Information
** <code>getFilter()</code> returns a reference to the Info field information, a VcfRecordInfo object reference
** <code>passedAllFilters()</code> returns true if the FILTER field indicates <code>PASS</code>, false if not.
* Aditional Information
** <code>getInfo()</code> returns a reference to the filter information, a VcfRecordFilter object reference
* Genotype Information
** <code>getGenotypeInfo()</code> returns a reference to the information from the genotype fields, a VcfRecordGenotype object reference
** <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.

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