public class Minimap2Utils
@NotNull
public static java.util.Map<java.lang.Integer,net.maizegenetics.pangenome.api.ReferenceRange> getHapToRefRangeMap(@NotNull
HaplotypeGraph graph)
Function to create a HapId to RefRange mapping for all of the HapIds in a graph
@NotNull
public static java.util.Map<java.lang.Integer,java.lang.Integer> getHapIdToSequenceLength(@NotNull
HaplotypeGraph graph)
@NotNull
public static java.util.Map<java.lang.Integer,java.util.Map> getRefRangeToHapidMap(@NotNull
HaplotypeGraph graph)
public static int getHaplotypeListIdForGraph(@NotNull
HaplotypeGraph graph,
@NotNull
PHGdbAccess phgAccessor)
public static boolean filterRead(@NotNull
htsjdk.samtools.SAMRecord currentSamRecord,
boolean pairedEnd,
boolean clippingFilter)
@NotNull public static ReadMappingKeyFileParsed loadInReadMappingKeyFile(@NotNull java.lang.String keyFileName, @NotNull ReadMappingInputFileFormat inputFileFormat, @NotNull java.lang.String inputFileDir, @NotNull java.lang.String methodName)
@NotNull
public static htsjdk.samtools.SamReader loadSAMFileIntoSAMReader(@NotNull
java.lang.String fileName)
Function to load the SAM file into a SAM reader Could remove this, but we should leave it in as you may need to read from a file in the future.
public static void runMinimapFromKeyFile(@NotNull
java.lang.String minimapLocation,
@NotNull
java.lang.String keyFileName,
@NotNull
java.lang.String inputFileDir,
@NotNull
java.lang.String referenceFile,
@Nullable
HaplotypeGraph graph,
double maxRefRangeError,
@NotNull
java.lang.String methodName,
@Nullable
java.lang.String methodDescription,
@NotNull
java.util.Map<java.lang.String,java.lang.String> pluginParams,
@NotNull
java.lang.String outputDebugReadMappingDir,
boolean outputSecondaryMappingStats,
int maxSecondary,
@NotNull
ReadMappingInputFileFormat inputFileFormat,
@NotNull
java.lang.String fParameter,
boolean isTestMethod,
boolean updateDB,
boolean runWithoutGraph,
@NotNull
java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> hapIdToRefRangeMap,
@NotNull
java.util.Map<java.lang.Integer,java.lang.Integer> hapIdToLengthMap,
@NotNull
java.util.Map<java.lang.Integer,? extends java.util.Map<java.lang.Integer,java.lang.Integer>> refRangeToHapIdMap,
@NotNull
java.lang.String inputFileName)
Method to run minimap2 using information provided by the Key file.
This assumes that there must be a column named filename and if paired end is requested a column named filename2.
There are additional pieces of information that will also be provided by the keyfile, but will be implemented once the DB changes are implemented.
public static void outputKeyFiles(@NotNull
java.lang.String keyFileName,
@NotNull
java.util.List<? extends java.util.List<java.lang.String>> keyFileLines,
int flowcellCol,
@NotNull
PHGdbAccess phg,
int taxonCol,
@NotNull
java.lang.String methodName,
@NotNull
java.util.Map<java.lang.String,java.lang.Integer> keyFileColumnNameMap)
Function to output mapping id and path key files to be used by the path finding.
public static void loadReadMappingsToDB(@NotNull
java.util.Map<java.util.List,java.lang.Integer> hapIdMapping,
@NotNull
java.lang.String taxon,
@NotNull
java.lang.String fileGroupName,
@NotNull
java.util.Map<java.lang.String,java.lang.String> pluginParams,
@Nullable
java.lang.String methodDescription,
@NotNull
PHGdbAccess phg,
@NotNull
java.lang.String methodName,
@NotNull
java.util.Map<net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord,java.lang.Integer> keyFileRecordsToMappingId,
@NotNull
KeyFileUniqueRecord keyFileRecord,
@NotNull
java.lang.String outputDebugReadMappingDir,
boolean isTestMethod,
int hapListId,
@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)
Function to load the Read Mappings to the DB. This will encode the ReadMappings and the load them in given the provided information.
@NotNull
public static kotlin.Pair<java.util.Map,java.util.List> readInKeyFile(@NotNull
java.lang.String fileName)
Function to read in the key file. The first of the pair is the column mapping and the second is a 2-d list.
public static void verifyNoDuplicatesInKeyFile(@NotNull
java.util.List<net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord> keyFileRecords)
verify that there are no duplicate entries in the key file. This is just to let the user know if there is a duplicate.
public static boolean isKeyEntryInDir(@NotNull
NonExistentClass fileNames,
@NotNull
java.util.List<java.lang.String> currentKeyRecord,
int fileCol1,
int fileCol2)
Method to check to see if there are missing files found in the key file but are missing in the Directory. If they are its ok, we expect the keyfile to have more entries than the directory.
@NotNull
public static htsjdk.samtools.SamReader setupMinimapRun(@NotNull
java.lang.String minimapLocation,
@NotNull
java.lang.String referenceFile,
@NotNull
java.lang.String firstFastq,
@NotNull
java.lang.String secondFastq,
int maxSecondary,
@NotNull
java.lang.String fParameter)
Function that sets up the paired or single end minimap commands and builds the SamReader
The SamReader is used later to pick optimal hits from the alignments.
If secondFastq is "", this will assume that single end is what needs to be run
@NotNull
public static java.util.Map<java.util.List,java.lang.Integer> scoreSamFileCountHapSetHits(@NotNull
htsjdk.samtools.SamReader samReader,
@NotNull
java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> hapIdToRefRangeMap,
double maxRefRangeError,
boolean pairedEnd,
@NotNull
java.lang.String outputDebugFile,
@NotNull
java.util.Map<java.lang.Integer,java.lang.Integer> hapIdToLengthMap)
Function to score a sam record. This will output a Map
For each subset of hapids we return a count of how many reads hit that exact subset. This mapping is used in the HMM.
public static void exportHapIdStats(@NotNull
java.lang.String outputDebugFile,
@NotNull
java.util.Map<java.lang.Integer,net.maizegenetics.pangenome.hapCalling.HapIdStats> hapIdToStatMap,
@NotNull
java.util.Map<java.lang.Integer,java.lang.Integer> hapIdToLengthMap)
Function to export the HapIdStats file. If outputDebugFile is not specified, this will do nothing.
public static void attemptToAddSAMRecordToBestReadMap(boolean pairedEnd,
@NotNull
htsjdk.samtools.SAMRecord currentSamRecord,
@NotNull
java.lang.String readName,
@NotNull
java.util.Map<kotlin.Pair,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup> bestReadMap)
Function to try to add a SAM record to bestReadMap. bestReadMap holds the currently best know set of reads which have the best(lowest) NM. If the current Record is better, we replace the old entry with a new one. If the current Record is the same, we add it to the list If the current Record is worse, we ignore.
public static void addBestReadMapToHapIdMultiset(@NotNull
java.util.Map<kotlin.Pair,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup> bestReadMap,
@NotNull
java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> hapIdToRefRangeMap,
double maxRefRangeError,
boolean pairedEnd,
@NotNull
HapIdMultiset hapIdMultiset,
@NotNull
java.util.Map<java.lang.Integer,net.maizegenetics.pangenome.hapCalling.HapIdStats> hapIdToStatMap)
@NotNull
public static java.util.Map<kotlin.Pair,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup> keepHapIdsForSingleRefRange(@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,
double maxRefRangeError)
Function to keep hapids if they are hitting multiple reference ranges too frequently. If there is a little bit of noise it can be filtered.
public static boolean spansSingleRefRange(@NotNull
java.util.Map.Entry<kotlin.Pair,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup> currentMapping,
@NotNull
java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> hapIdToRangeMap)
Function to check to see if the reads only hit one reference range
@NotNull
public static kotlin.Pair<kotlin.Pair,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup> removeExtraRefRangeHits(@NotNull
java.util.Map.Entry<kotlin.Pair,net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup> currentMapping,
@NotNull
java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> hapIdToRangeMap,
double maxRefRangeError)
Function to remove any reads which hit more than one reference range ambiguously.
public static int findBestRefRange(@NotNull
com.google.common.collect.Multimap<java.lang.Integer,java.lang.Integer> refRangeToIdMapping,
double maxRefRangeError)
Function to check to see if the read hits a multiple reference ranges less than maxRefRangeError Basically this is to filter out any reads which hit multiple reference ranges equally well