net.maizegenetics.pangenome.processAssemblyGenomes

Class AssemblyProcessingUtils

java.lang.Object

net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils

public class AssemblyProcessingUtils
extends Object

This class contains methods useful for processing assembly haplotypes.

Author:

lcj34

Constructor Summary

Constructors

Constructor and Description
AssemblyProcessingUtils()

Method Summary

Modifier and Type	Method and Description
static double	calculateCoordDistance(net.maizegenetics.util.Tuple<Integer,Integer> prev, net.maizegenetics.util.Tuple<Integer,Integer> current) Calculates distance between 2 sets of mummer coords file entries This is called on coordinates that are both either ascending (start < end) or both descending (start > end) so "sign" of entries is not checked here.
static boolean	checkSnpEntryInRange(String mline, com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,List<net.maizegenetics.dna.map.Position>> coordsRangeMap, String chrom) Verifies if the positions from a Mummer4 snp file fall within the range map of reference and assembly positions created from the Mummer4 coordinates files.
static void	exportMergedRegions(Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>> mergedCoords, String fileName) Deprecated.
static List<htsjdk.variant.variantcontext.VariantContext>	extractAnchorVariantContextsFromAssemblyAlignments(net.maizegenetics.dna.map.GenomeSequence refSequence, String assemblyName, com.google.common.collect.RangeSet<net.maizegenetics.dna.map.Position> anchors, Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>> refMappings, com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<String,String>> snps) Method to build the list of VariantContexts based on the mapped coordinates and the SNPs
static int	findAsmIndelStart(Collection<String> snpEntries)
static net.maizegenetics.util.Tuple<Integer,Integer>	findRefIndelStart(int refSnpPos, Collection<String> snpEntries) Find the lowest reference start entry from a mummer snp file list of entries.
static List<htsjdk.variant.variantcontext.VariantContext>	findVCListForAnchor(List<htsjdk.variant.variantcontext.VariantContext> variantContextList, int refStart, int refEnd) Find a subset of the VariantContext.
static com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,List<net.maizegenetics.dna.map.Position>>	getCoordsRangeMap(List<String> coordsList, String chrom) Create range map from list of entries from a Mummer coordinates file
static String	getEntryFromTabDelimitedLine(String mline, int entryColumn, int totalColumns) Returns the value for a specific column in a tab-delimited string
static com.google.common.collect.RangeSet<net.maizegenetics.dna.map.Position>	getIndelRanges(com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,List<net.maizegenetics.dna.map.Position>> coordinates)
static net.maizegenetics.util.Tuple<Integer,Double>	getRegionCoverage(com.google.common.collect.RangeSet<Integer> rangeSet, com.google.common.collect.Range<Integer> targetRange) This method takes a RangeSet of integers, and a single range.
static net.maizegenetics.util.Tuple<Integer,Integer>	getStartEndCoordinates(String entry, boolean ref) Find the start/end coordinates from a tab-delmimited Mummer4 coords file entry
static boolean	isRefBlock(htsjdk.variant.variantcontext.VariantContext vc) Simple method to determine if the current variant context is a reference block or not.
static Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>>	mergeCoords(String coordFile, String chromosome) Deprecated.
static Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>>	parseCoordinateRegions(String coordFile, String chromosome) Method to parse out the reference coordinates into a map which along with the SNP data can then be used to create Variants.
static com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<String,String>>	parseMummerSNPFile(String fileName, String chromosome) Method to parse the Mummer SNP file into a rangemap The first String in the tuple is for the reference call The second String is for the assembly call
static Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>>	resizeCoords(String coordFile, String chromosome) Test method to resize the coordinate files so they are not overlapping
static List<htsjdk.variant.variantcontext.VariantContext>	resizeRefBlock(htsjdk.variant.variantcontext.VariantContext vc, net.maizegenetics.dna.map.GenomeSequence refSequence, net.maizegenetics.dna.map.Position positionToSplit, boolean isStart) Method which will take a variant Context which needs to be split and will output 2 new variants while updating ASM_* annotations.
static com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<String,String>>	setupIndelVariants(Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>> coordinates, net.maizegenetics.dna.map.GenomeSequence refSequence, net.maizegenetics.dna.map.GenomeSequence asmSequence) Method to fill in the unmapped regions coming from nucmer.
static List<htsjdk.variant.variantcontext.VariantContext>	splitRefRange(List<htsjdk.variant.variantcontext.VariantContext> variantContexts, Map<Integer,ReferenceRange> anchorMapping, net.maizegenetics.dna.map.GenomeSequence refSequence) Method to split up the reference range by anchor mappings.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AssemblyProcessingUtils

public AssemblyProcessingUtils()

Method Detail

getCoordsRangeMap

public static com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,List<net.maizegenetics.dna.map.Position>> getCoordsRangeMap(List<String> coordsList,
                                                                                                                                                String chrom)

Create range map from list of entries from a Mummer coordinates file

Parameters:

coordsList - List containing tab-delimited strings from a Mummer coordinates file

chrom - String with chromosome name

Returns:

RangeMap: A rangemap of the coordinate values form the mummer coords file list

getEntryFromTabDelimitedLine

public static String getEntryFromTabDelimitedLine(String mline,
                                                  int entryColumn,
                                                  int totalColumns)

Returns the value for a specific column in a tab-delimited string

Parameters:

mline -

entryColumn - - the column number (1-based) of the entry the caller wants

totalColumns - - total number of tab-delimited columns in the line

Returns:

String containing the column contents

getStartEndCoordinates

public static net.maizegenetics.util.Tuple<Integer,Integer> getStartEndCoordinates(String entry,
                                                                                   boolean ref)

Find the start/end coordinates from a tab-delmimited Mummer4 coords file entry

Parameters:

entry: - Line from a mummer coords file

ref - Boolean: if true, get ref start end. Otherwise, get assembly start/end

Returns:

calculateCoordDistance

public static double calculateCoordDistance(net.maizegenetics.util.Tuple<Integer,Integer> prev,
                                            net.maizegenetics.util.Tuple<Integer,Integer> current)

Calculates distance between 2 sets of mummer coords file entries This is called on coordinates that are both either ascending (start < end) or both descending (start > end) so "sign" of entries is not checked here.

Parameters:

prev -

current -

Returns:

checkSnpEntryInRange

public static boolean checkSnpEntryInRange(String mline,
                                           com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,List<net.maizegenetics.dna.map.Position>> coordsRangeMap,
                                           String chrom)

Verifies if the positions from a Mummer4 snp file fall within the range map of reference and assembly positions created from the Mummer4 coordinates files.

Parameters:

mline -

Returns:

findVCListForAnchor

public static List<htsjdk.variant.variantcontext.VariantContext> findVCListForAnchor(List<htsjdk.variant.variantcontext.VariantContext> variantContextList,
                                                                                     int refStart,
                                                                                     int refEnd)

Find a subset of the VariantContext. Return only those in the list that fall within (inclusive) the start/end range given. This assume the VC is 1-based inclusive/inclusive as are the start/end parameters

Parameters:

variantContextList -

refStart -

refEnd -

Returns:

getRegionCoverage

public static net.maizegenetics.util.Tuple<Integer,Double> getRegionCoverage(com.google.common.collect.RangeSet<Integer> rangeSet,
                                                                             com.google.common.collect.Range<Integer> targetRange)

This method takes a RangeSet of integers, and a single range. It finds all the ranges in the set that intersect the targetRange. Calculate both the number of bases from the targetRange that are represented in the rangeSet, and the percentage of the bases represented. Return a Tuple with this information.

Parameters:

rangeSet -

targetRange -

Returns:

parseMummerSNPFile

public static com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<String,String>> parseMummerSNPFile(String fileName,
                                                                                                                                                    String chromosome)

Method to parse the Mummer SNP file into a rangemap The first String in the tuple is for the reference call The second String is for the assembly call

Parameters:

fileName -

chromosome -

Returns:

parseCoordinateRegions

public static Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>> parseCoordinateRegions(String coordFile,
                                                                                                                                                       String chromosome)

Method to parse out the reference coordinates into a map which along with the SNP data can then be used to create Variants.

Parameters:

coordFile -

chromosome -

Returns:

mergeCoords

@Deprecated
public static Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>> mergeCoords(String coordFile,
                                                                                                                                                        String chromosome)

Deprecated.

Test method to try to merge overlapping coordinates. We thought Show-SNPs would recall the SNPs in the delta file based on this information, but this was not the case.

Parameters:

coordFile -

chromosome -

Returns:

resizeCoords

public static Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>> resizeCoords(String coordFile,
                                                                                                                                             String chromosome)

Test method to resize the coordinate files so they are not overlapping

Parameters:

coordFile -

chromosome -

Returns:

exportMergedRegions

@Deprecated
public static void exportMergedRegions(Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>> mergedCoords,
                                                   String fileName)

Deprecated.

Utility method to export out the merged regions

Parameters:

mergedCoords -

fileName -

setupIndelVariants

public static com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<String,String>> setupIndelVariants(Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>> coordinates,
                                                                                                                                                    net.maizegenetics.dna.map.GenomeSequence refSequence,
                                                                                                                                                    net.maizegenetics.dna.map.GenomeSequence asmSequence)

Method to fill in the unmapped regions coming from nucmer. This method will create multi-bp indels between the mapped regions which can then be added to the SNP list for processing into Variants.

Parameters:

coordinates -

refSequence -

asmSequence -

Returns:

getIndelRanges

public static com.google.common.collect.RangeSet<net.maizegenetics.dna.map.Position> getIndelRanges(com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,List<net.maizegenetics.dna.map.Position>> coordinates)

extractAnchorVariantContextsFromAssemblyAlignments

public static List<htsjdk.variant.variantcontext.VariantContext> extractAnchorVariantContextsFromAssemblyAlignments(net.maizegenetics.dna.map.GenomeSequence refSequence,
                                                                                                                    String assemblyName,
                                                                                                                    com.google.common.collect.RangeSet<net.maizegenetics.dna.map.Position> anchors,
                                                                                                                    Map<com.google.common.collect.Range<net.maizegenetics.dna.map.Position>,List<net.maizegenetics.dna.map.Position>> refMappings,
                                                                                                                    com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<String,String>> snps)

Method to build the list of VariantContexts based on the mapped coordinates and the SNPs

Parameters:

refSequence -

assemblyName -

anchors -

refMappings -

snps -

Returns:

splitRefRange

public static List<htsjdk.variant.variantcontext.VariantContext> splitRefRange(List<htsjdk.variant.variantcontext.VariantContext> variantContexts,
                                                                               Map<Integer,ReferenceRange> anchorMapping,
                                                                               net.maizegenetics.dna.map.GenomeSequence refSequence)

Method to split up the reference range by anchor mappings. Basically this method will take the variant contexts and the anchor coordinates. If a variant context is a reference block which is spanning the start or end of the anchor(should happen frequently if anchor ends are truly conserved), we need to break up the variant context into two adjacent reference blocks with the end point being the start or end of one of the variants. This will allow for easy querying of the list of Variants when attempting to load into the db.

Parameters:

variantContexts -

anchorMapping -

refSequence -

Returns:

isRefBlock

public static boolean isRefBlock(htsjdk.variant.variantcontext.VariantContext vc)

Simple method to determine if the current variant context is a reference block or not.

Parameters:

vc -

Returns:

resizeRefBlock

public static List<htsjdk.variant.variantcontext.VariantContext> resizeRefBlock(htsjdk.variant.variantcontext.VariantContext vc,
                                                                                net.maizegenetics.dna.map.GenomeSequence refSequence,
                                                                                net.maizegenetics.dna.map.Position positionToSplit,
                                                                                boolean isStart)

Method which will take a variant Context which needs to be split and will output 2 new variants while updating ASM_* annotations. Depending on if the splitting position is a start or end or if the assembly is increasing or decreasing, it will have to handle things differently.

Parameters:

vc -

refSequence -

positionToSplit -

isStart -

Returns:

findRefIndelStart

public static net.maizegenetics.util.Tuple<Integer,Integer> findRefIndelStart(int refSnpPos,
                                                                              Collection<String> snpEntries)

Find the lowest reference start entry from a mummer snp file list of entries. There could be more than 1 string of indels for this asm snp. Find the start and end of the string of indels whose positions overlap the reference position for the SNP in question. Return the start position and the length of this string of indels

Parameters:

refSnpPos -

snpEntries -

Returns:

findAsmIndelStart

public static int findAsmIndelStart(Collection<String> snpEntries)