LibStatGen: VCF - Revision history

Youna at 20:09, 23 January 2013

2013-01-23T20:09:56Z

← Older revision		Revision as of 16:09, 23 January 2013
Line 19:		Line 19:
	<code>VcfFileReader</code> is declared in <code>VcfFileReader.h</code>, so be sure to include that file.		<code>VcfFileReader</code> is declared in <code>VcfFileReader.h</code>, so be sure to include that file.
	<source lang="cpp">		<source lang="cpp">
	#include "~~AspFileReader~~.h"		#include "VcfFileReader.h"
	</source>		</source>

Mktrost: /* Specifying Discard Rules */

2012-07-25T20:57:17Z

Specifying Discard Rules

@@ Line 140: / Line 140: @@
 VcfFileReader::rmDiscardMinAltAlleleCount()
 </source>
 ===== Minimum Minor Allele Count =====
@@ Line 157: / Line 174: @@
 VcfFileReader::rmDiscardMinMinorAlleleCount()
 </source>
 ==== Read only Certain Sections of the File / Using a VCF Index (TABIX) File ====

Mktrost at 20:47, 25 July 2012

2012-07-25T20:47:03Z

@@ Line 37: / Line 37: @@
 </source>
-==== Subsetting Samples ====
+==== Reading a Subset of 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').
 <source lang="cpp">
@@ Line 134: / Line 134: @@
 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:
+See [[#Handling a Subset of Samples|Handling a Subset of Samples]] for how to use <code>VcfSubsetSamples</code>.
 Use the following method to remove the DiscardMinAltAlleleCount rule:
@@ Line 164: / Line 151: @@
 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:
+See [[#Handling a Subset of Samples|Handling a Subset of Samples]] for how to use <code>VcfSubsetSamples</code>.
 Use the following method to remove the DiscardMinMinorAlleleCount rule:
@@ Line 309: / Line 283: @@
 === VcfRecordFilter ===
 <code>VcfRecords</code> contain the data from the <code>INFO</code> field in a <code>VcfRecordFilter</code> object.

Mktrost: /* Minimum Alternate Allele Count */

2012-07-25T20:34:44Z

Minimum Alternate Allele Count

@@ Line 125: / Line 125: @@
 ===== Minimum Alternate Allele Count =====
 To Discard any records without a minimum number of alternate alleles, use:
 <source lang="cpp">
@@ Line 154: / Line 152: @@
 <source lang="cpp">
 VcfFileReader::rmDiscardMinAltAlleleCount()
 </source>

Mktrost: /* Extracting Data from the Record */

2012-07-24T14:48:12Z

Extracting Data from the Record

← Older revision		Revision as of 10:48, 24 July 2012
Line 274:		Line 274:
	** <code>allPhased()</code> returns true if all the samples are phased and none unphased and false if any are not phased		** <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>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.		** <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
			** <code>getNumSamples()</code> returns the number of samples (that are kept)
			** <code>getNumGTs(int index)</code> returns the number of GTs for the specified sample index (starts at 0)
			** <code>getGT(int sampleNum, unsigned int gtIndex)</code> returns the integer GT value for the specified sampleNum and GT index (both start at 0). A GT of VcfGenotypeSample::INVALID_GT is returned if the sampleNum or GT index is out of range. A GT of VcfGenotypeSample::MISSING_GT if the GT is '.' (This method is also found in VcfRecordGenotype.

	=== VcfRecordFilter ===		=== VcfRecordFilter ===
	<code>VcfRecords</code> contain the data from the <code>INFO</code> field in a <code>VcfRecordFilter</code> object.		<code>VcfRecords</code> contain the data from the <code>INFO</code> field in a <code>VcfRecordFilter</code> object.

Mktrost: /* Additional Rules */

2012-07-24T14:42:49Z

Additional Rules

← Older revision		Revision as of 10:42, 24 July 2012
Line 124:		Line 124:
	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~~ =====		===== 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>

	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.

	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>

	Use the following method to remove the DiscardMinAltAlleleCount rule:		Use the following method to remove the DiscardMinAltAlleleCount rule:

Mktrost: /* Additional Rules */

2012-07-24T14:28:42Z

Additional Rules

← Older revision		Revision as of 10:28, 24 July 2012
Line 135:		Line 135:

	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>minAltAlleleCount</code> parameter is the minimum number of alternate alleles found in the subset in order for the record to be kept.

			Use the following method to remove the DiscardMinAltAlleleCount rule:
			<source lang="cpp">
			VcfFileReader::rmDiscardMinAltAlleleCount()
			</source>

	==== 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 ====

Mktrost: /* Specifying Discard Rules */

2012-07-24T14:27:51Z

Specifying Discard Rules

← Older revision		Revision as of 10:27, 24 July 2012
Line 101:		Line 101:

	==== 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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	</source>		</source>
	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 ====

Mktrost: /* Subsetting Samples */

2012-06-13T15:07:42Z

Subsetting Samples

@@ Line 44: / Line 44: @@
      VcfHeader header;
      // Subset 1 is delimited by new lines, '\n'.
-     reader.open("vcfFileName.vcf", header, "subsetFile1.txt");
+     reader.open("vcfFileName.vcf", header, "subsetFile1.txt", NULL, NULL);
 </source>
 <source lang="cpp">
@@ Line 51: / Line 51: @@
      VcfHeader header;
      // Subset 2 is delimited by ';'
-     reader.open("vcfFileName.vcf", header, "subsetFile2.txt", ';');
+     reader.open("vcfFileName.vcf", header, "subsetFile2.txt", NULL, NULL, ';');
 </source>

Mktrost: /* Read only Certain Sections of the File / Using a VCF Index (TABIX) File */

2012-04-18T22:12:55Z

Read only Certain Sections of the File / Using a VCF Index (TABIX) File

← Older revision		Revision as of 18:12, 18 April 2012
Line 118:		Line 118:
	bool setReadSection(const char* chromName);		bool setReadSection(const char* chromName);
	bool set1BasedReadSection(const char* chromName,		bool set1BasedReadSection(const char* chromName,
	int32_t start, int32_t end);		int32_t start, int32_t end,
			bool overlap = false);
	</source>		</source>
	Both methods currently always return true, since in the current implementation this can't fail. It currently allows the VcfIndex file to be read after this call.		Both methods currently always return true, since in the current implementation this can't fail. It currently allows the VcfIndex file to be read after this call.
Line 127:		Line 128:

	<code>set1BasedReadSection</code> will set the code to read the specified chromosome starting at the specified 1-based position up to, but not including, the specified 1-based end position. On the first <code>readRecord</code> call it will jump the file to the beginning of this section. It will continue to read the section for each <code>readRecord</code> call made until it has read the entire section. Once the entire section has been read, <code>readRecord</code> will return false until a new read section is specified.		<code>set1BasedReadSection</code> will set the code to read the specified chromosome starting at the specified 1-based position up to, but not including, the specified 1-based end position. On the first <code>readRecord</code> call it will jump the file to the beginning of this section. It will continue to read the section for each <code>readRecord</code> call made until it has read the entire section. Once the entire section has been read, <code>readRecord</code> will return false until a new read section is specified.

			<code>set1BasedReadSection</code> takes an optional parameter, <code>overlap</code>. It is defaulted to false which means that only records that start within the specified region will be returned by <code>readRecord</code>. If <code>overlap</code> is set to true, <code>readRecord</code> will also return records that start prior to the specified region, but whose deletions occur in the specified region.

	Implementation NOTE: internally it may read extra records prior to the section, but <code>readRecord</code> will keep reading and will not return until it finds a record in the section or until the section has been passed (no records in the section).		Implementation NOTE: internally it may read extra records prior to the section, but <code>readRecord</code> will keep reading and will not return until it finds a record in the section or until the section has been passed (no records in the section).