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Fixing docs and adding GATKdocs for the new interval functionality

This commit is contained in:
Eric Banks 2011-10-26 22:14:43 -04:00
parent 2f21b6ecfb
commit 68283b1651
3 changed files with 28 additions and 11 deletions
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35
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -81,22 +81,38 @@ public class GATKArgumentCollection {
public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD;
@ElementList(required = false)
@Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually.", required = false)
@Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false)
public List<String> readFilters = new ArrayList<String>();
/**
* Using this option one can instruct the GATK engine to traverse over only part of the genome. This argument can be specified multiple times.
* One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals).
* Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf).
*/
@ElementList(required = false)
@Input(fullName = "intervals", shortName = "L", doc = "A list of genomic intervals over which to operate. Can be explicitly specified on the command line or in a file.", required = false)
@Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
public List<IntervalBinding<Feature>> intervals = null;
/**
* Using this option one can instruct the GATK engine NOT to traverse over certain parts of the genome. This argument can be specified multiple times.
* One may use samtools-style intervals either explicitly (e.g. -XL chr1 or -XL chr1:100-200) or listed in a file (e.g. -XL myFile.intervals).
* Additionally, one may specify a rod file to skip over the positions for which there is a record in the file (e.g. -XL file.vcf).
*/
@ElementList(required = false)
@Input(fullName = "excludeIntervals", shortName = "XL", doc = "A list of genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file.", required = false)
@Input(fullName = "excludeIntervals", shortName = "XL", doc = "One or more genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
public List<IntervalBinding<Feature>> excludeIntervals = null;
/**
* How should the intervals specified by multiple -L or -XL arguments be combined? Using this argument one can, for example, traverse over all of the positions
* for which there is a record in a VCF but just in chromosome 20 (-L chr20 -L file.vcf -isr INTERSECTION).
*/
@Element(required = false)
@Argument(fullName = "interval_set_rule", shortName = "isr", doc = "Indicates the set merging approach the interval parser should use to combine the various -L inputs", required = false)
@Argument(fullName = "interval_set_rule", shortName = "isr", doc = "Indicates the set merging approach the interval parser should use to combine the various -L or -XL inputs", required = false)
public IntervalSetRule intervalSetRule = IntervalSetRule.UNION;
/** What rule should we use when merging intervals */
/**
* Should abutting (but not overlapping) intervals be treated as separate intervals?
*/
@Element(required = false)
@Argument(fullName = "interval_merging", shortName = "im", doc = "Indicates the interval merging rule we should use for abutting intervals", required = false)
public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL;
@ -125,7 +141,7 @@ public class GATKArgumentCollection {
private static int DEFAULT_DOWNSAMPLING_COVERAGE = 1000;
@Element(required = false)
@Argument(fullName = "downsampling_type", shortName="dt", doc="Type of reads downsampling to employ at a given locus. Reads will be selected randomly to be removed from the pile based on the method described here.", required = false)
@Argument(fullName = "downsampling_type", shortName="dt", doc="Type of reads downsampling to employ at a given locus. Reads will be selected randomly to be removed from the pile based on the method described here", required = false)
public DownsampleType downsamplingType = null;
@Element(required = false)
@ -207,13 +223,12 @@ public class GATKArgumentCollection {
@Argument(fullName = "unsafe", shortName = "U", doc = "If set, enables unsafe operations: nothing will be checked at runtime. For expert users only who know what they are doing. We do not support usage of this argument.", required = false)
public ValidationExclusion.TYPE unsafe;
/** How many threads should be allocated to this analysis. */
@Element(required = false)
@Argument(fullName = "num_threads", shortName = "nt", doc = "How many threads should be allocated to running this analysis.", required = false)
@Argument(fullName = "num_threads", shortName = "nt", doc = "How many threads should be allocated to running this analysis", required = false)
public int numberOfThreads = 1;
@ElementList(required = false)
@Input(fullName = "read_group_black_list", shortName="rgbl", doc="Filters out read groups matching <TAG>:<STRING> or a .txt file containing the filter strings one per line.", required = false)
@Input(fullName = "read_group_black_list", shortName="rgbl", doc="Filters out read groups matching <TAG>:<STRING> or a .txt file containing the filter strings one per line", required = false)
public List<String> readGroupBlackList = null;
// --------------------------------------------------------------------------------------------------------------
@ -310,7 +325,7 @@ public class GATKArgumentCollection {
public boolean allowIntervalsWithUnindexedBAM = false;
@Element(required = false)
@Argument(fullName="disable_experimental_low_memory_sharding",doc="Disable experimental low-memory sharding functionality.",required=false)
@Argument(fullName="disable_experimental_low_memory_sharding",doc="Disable experimental low-memory sharding functionality",required=false)
public boolean disableLowMemorySharding = false;
// --------------------------------------------------------------------------------------------------------------

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
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@ -53,7 +53,7 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
}
public enum GENOTYPING_MODE {
/** the default; the Unified Genotyper will choose the most likely alternate allele */
/** the Unified Genotyper will choose the most likely alternate allele */
DISCOVERY,
/** only the alleles passed in from a VCF rod bound to the -alleles argument will be used for genotyping */
GENOTYPE_GIVEN_ALLELES

2
public/java/src/org/broadinstitute/sting/utils/interval/IntervalSetRule.java
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@ -4,6 +4,8 @@ package org.broadinstitute.sting.utils.interval;
* set operators for combining lists of intervals
*/
public enum IntervalSetRule {
/** Take the union of all intervals */
UNION,
/** Take the intersection of intervals (the subset that overlaps all intervals specified) */
INTERSECTION;
}