public class ReadMappingUtils
@Nullable
public static kotlin.Array[] encodeHapIdMapping(@NotNull
java.util.Map<java.util.List,java.lang.Integer> hapIdMapping)
Function to encode the HapId Map into a byte array and compress it.
@Nullable
public static kotlin.Array[] encodeHapIdsAsBitSet(@NotNull
java.util.Map<java.util.List,java.lang.Integer> hapIdMapping,
@NotNull
java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> hapIdToRefRangeMap,
@NotNull
java.util.Map<java.lang.Integer,? extends java.util.Map<java.lang.Integer,java.lang.Integer>> refRangeToHapIdMap)
Encodes haplotypeSet counts by first translating each haplotypeSet into a BitSet.
hapIdMapping maps a list of haplotype ids to their counts.
hapIdToRefRangeMap is a map of haplotype id to ReferenceRange.
refRangeToHapIdMap maps refRangeId to a map of haplotype id to its index,
where the index represents the order of the haplotype ids in that ReferenceRange,
The haplotype ids in each reference range are indexed in ascending order.
hapIdMapping,
hapIdToRefRangeMap,
refRangeToHapIdMap@NotNull
public static java.util.List<java.lang.Integer> bitSetToIntList(@NotNull
java.util.BitSet bitSet)
@NotNull
public static java.util.Map<java.util.List,java.lang.Integer> decodeHapIdMapping(@NotNull
kotlin.Array[] encodedReadMapping)
Function to decode the HapId byte array into the Mapping to be used by Path Finding.
public static void exportReadMapping(@NotNull
java.lang.String outputFileName,
@NotNull
java.util.Map<java.util.List,java.lang.Integer> hapIdMapping,
@NotNull
java.lang.String taxon,
@NotNull
java.lang.String fileGroupName,
@NotNull
java.lang.String methodName,
@NotNull
java.lang.String methodDescription)
Function to export the read mapping files to disk. This is mostly for debugging purposes.
@NotNull
public static com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.HapIdSetCount> readInReadMappings(@NotNull
java.lang.String inputFileName,
@NotNull
HaplotypeGraph graph)
@NotNull
public static java.util.Map<java.util.List,java.lang.Integer> importReadMapping(@NotNull
java.lang.String inputFileName)
Function to read in the Readmapping file into a Map
public static void exportBestHitMap(@NotNull
java.util.Map<kotlin.Pair,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup> bestHitMap,
@NotNull
java.lang.String readMappingFile)
Function to export the best hit mapping. This allows for easier debugging.
public static void exportMultimap(@NotNull
com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.SingleHapMapping> bestMapping,
@NotNull
java.lang.String outputFileName)
Function to write out the multimap data structure to a file. This requires the whole multimap to be constructed first
@NotNull
public static java.util.List<kotlin.Pair> convertHitMapToSingleHapMapping(@NotNull
java.util.Set<java.lang.String> readNames,
@NotNull
java.util.Map<kotlin.Pair,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup> bestHitMap,
@NotNull
java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> hapIdToRangeMap,
@NotNull
kotlin.jvm.functions.Function2<? super java.lang.String,? super java.util.Map<kotlin.Pair<java.lang.String,java.lang.Boolean>,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup>,java.lang.Boolean> filterFunction,
@NotNull
kotlin.jvm.functions.Function2<? super java.lang.String,? super java.util.Map<kotlin.Pair<java.lang.String,java.lang.Boolean>,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup>,? extends kotlin.Pair<java.lang.String,? extends java.util.Set<java.lang.Integer>>> mapToListFunction)
Function to do some filtering on read mappings then will convert the mappings into the correct datastructure for the multimaps
This can handle both paired end and single ends depending on the mapping functions passed in.
The first is a filter function takes a String for the readName and the Mapping
The second function is a mapping function which creates a Pair
For instance in paired end mode, the filter function makes sure that both strand reads are represented in the map And the mapping function will take the intersection of the hapids for both strands which helps remove the bad mapping regions
The single end is basically making sure that the read name is in the Map and the mapping function will just take the hapIds and put it in a Pair
@NotNull
public static com.google.common.collect.Multimap<java.lang.String,java.lang.String> readInMultimapHitsFromFile(@NotNull
java.lang.String inputFileName)
Function to read in the multimapHits from a text file.
@NotNull
public static com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.SingleHapMapping> readInListOfMultimapHits(@NotNull
java.util.List<java.lang.String> inputFiles,
@NotNull
HaplotypeGraph graph)
Function to read in the multimap Hits from a file and store it in a list. The graph is needed to get a refRangeId to RefRange mapping
@NotNull
public static com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.SingleHapMapping> readInListOfMultimapHits(@NotNull
java.util.List<java.lang.String> inputFiles,
@NotNull
java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> rangeIdToRangeMap)
Function to read in the Multimap
@NotNull
public static com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.SingleHapMapping> readInMultimapHits(@NotNull
java.lang.String inputFileName,
@NotNull
HaplotypeGraph graph)
Function to read in the multimap Hits from a file and store it in a Multimap. The graph is needed to get a refRangeId to RefRange mapping
@NotNull
public static com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.SingleHapMapping> readInMultimapHits(@NotNull
java.lang.String inputFileName,
@NotNull
java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> rangeIdToRangeMap)
Function to read in the multimap hits.
@NotNull
public static java.util.List<java.lang.String> getHaplotypeMethodsForReadMappings(@NotNull
com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.HapIdSetCount> readMap,
int numberOfRefRanges)
@NotNull
public static java.util.List<java.lang.String> getHaplotypeMethodForHapids(@NotNull
java.util.Collection<java.lang.Integer> hapidList)