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818 bytes added
, 10:42, 24 July 2012
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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. |
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− | ===== Additional Rules ===== | + | ===== Minimum Alternate Allele Count ===== |
| There are additional discard rules that can be specified by calling methods on VcfFileReader. | | There are additional discard rules that can be specified by calling methods on VcfFileReader. |
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| </source> | | </source> |
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− | 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 specified subset (if specified) in order for the record to be kept. |
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− | The <code>minAltAlleleCount</code> parameter is the minimum number of alternate alleles found in the subset 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 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: |
| + | <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> |
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| Use the following method to remove the DiscardMinAltAlleleCount rule: | | Use the following method to remove the DiscardMinAltAlleleCount rule: |