net.maizegenetics.pangenome.hapCalling

Class FilterBAMAndGetStatsPlugin

net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin

public class FilterBAMAndGetStatsPlugin

Plugin to Filter out the BAMs and build a stats file to get numbers of each of the CIGAR operators for each reference range as well as how many reads hit each one.

Constructor Detail

FilterBAMAndGetStatsPlugin

public FilterBAMAndGetStatsPlugin(@Nullable
                                  java.awt.Frame parentFrame,
                                  boolean isInteractive)

Plugin to Filter out the BAMs and build a stats file to get numbers of each of the CIGAR operators for each reference range as well as how many reads hit each one.

FilterBAMAndGetStatsPlugin

public FilterBAMAndGetStatsPlugin()

Plugin to Filter out the BAMs and build a stats file to get numbers of each of the CIGAR operators for each reference range as well as how many reads hit each one.

Method Detail

processData

@Nullable
public net.maizegenetics.plugindef.DataSet processData(@Nullable
                                                                 net.maizegenetics.plugindef.DataSet input)

processSAMRecords

public void processSAMRecords(@NotNull
                              htsjdk.samtools.SamReader samReader,
                              boolean pairedEnd,
                              @NotNull
                              java.util.Map<java.lang.Integer,java.lang.Integer> hapIdToRefRangeMap,
                              double maxRefRangeError,
                              @NotNull
                              java.lang.String outputBamFile,
                              @NotNull
                              java.lang.String outputStatsFile)

Function that processes the records within a SAM file similar to what is done in Minimap2Utils. This will keep track of the alignment stats as it is going and will output the correct values.

keepHapIdsForSingleRefRange

@NotNull
public java.util.Map<kotlin.Pair,java.util.List> keepHapIdsForSingleRefRange(@NotNull
                                                                                      java.util.Map<kotlin.Pair,? extends java.util.List<htsjdk.samtools.SAMRecord>> bestHitMap,
                                                                                      @NotNull
                                                                                      java.util.Map<java.lang.Integer,java.lang.Integer> hapIdToRangeMap,
                                                                                      double maxRefRangeError)

Simple function to remobve hapIds if they cross multiple reference ranges.

removeExtraRangeAlignments

@NotNull
public kotlin.Pair<kotlin.Pair,java.util.List> removeExtraRangeAlignments(@NotNull
                                                                                   java.util.Map.Entry<kotlin.Pair,? extends java.util.List<htsjdk.samtools.SAMRecord>> entry,
                                                                                   @NotNull
                                                                                   java.util.Map<java.lang.Integer,java.lang.Integer> hapIdToRangeMap,
                                                                                   double maxRefRangeError)

Simple function to go through the records grouped by range and remove any suboptimal alignments.

findBestRefRangeFromRecords

public int findBestRefRangeFromRecords(@NotNull
                                       java.util.Map<java.lang.Integer,? extends java.util.List<? extends htsjdk.samtools.SAMRecord>> 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

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

bamFile

@NotNull
public java.lang.String bamFile()

Name of the BAM file to process. Also will support SAM Files

Returns:

bamFile

bamFile

@NotNull
public FilterBAMAndGetStatsPlugin bamFile(@NotNull
                                                   java.lang.String value)

Set bamFile. Name of the BAM file to process. Also will support SAM Files

Parameters:

value - bamFile

Returns:

this plugin

outputBamFile

@NotNull
public java.lang.String outputBamFile()

Name of the output filtered BAM/SAM file.

Returns:

Output Bam File

outputBamFile

@NotNull
public FilterBAMAndGetStatsPlugin outputBamFile(@NotNull
                                                         java.lang.String value)

Set Output Bam File. Name of the output filtered BAM/SAM file.

Parameters:

value - Output Bam File

Returns:

this plugin

outputStatsFile

@NotNull
public java.lang.String outputStatsFile()

Name of the output stats file of RefRange to total counts.

Returns:

Output Stats File

outputStatsFile

@NotNull
public FilterBAMAndGetStatsPlugin outputStatsFile(@NotNull
                                                           java.lang.String value)

Set Output Stats File. Name of the output stats file of RefRange to total counts.

Parameters:

value - Output Stats File

Returns:

this plugin

isPairedEnd

public boolean isPairedEnd()

Flag to set if you are using Paired End reads.

Returns:

Is Paired End

isPairedEnd

@NotNull
public FilterBAMAndGetStatsPlugin isPairedEnd(boolean value)

Set Is Paired End. Flag to set if you are using Paired End reads.

Parameters:

value - Is Paired End

Returns:

this plugin

maxRefRangeError

public double maxRefRangeError()

Maximum allowed error when choosing best reference range to count. Error is computed 1 - (mostHitRefCount/totalHits)

Returns:

Max Ref Range Err

maxRefRangeError

@NotNull
public FilterBAMAndGetStatsPlugin maxRefRangeError(double value)

Set Max Ref Range Err. Maximum allowed error when choosing best reference range to count. Error is computed 1

• (mostHitRefCount/totalHits)

Parameters:

value - Max Ref Range Err

Returns:

this plugin