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, 16:34, 25 July 2012
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| ===== Minimum Alternate Allele Count ===== | | ===== Minimum Alternate Allele Count ===== |
− | There are additional discard rules that can be specified by calling methods on VcfFileReader.
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| To Discard any records without a minimum number of alternate alleles, use: | | To Discard any records without a minimum number of alternate alleles, use: |
| <source lang="cpp"> | | <source lang="cpp"> |
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| <source lang="cpp"> | | <source lang="cpp"> |
| VcfFileReader::rmDiscardMinAltAlleleCount() | | 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> | | </source> |
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