org.broadinstitute.hellbender.utils

Class IGVUtils

java.lang.Object

org.broadinstitute.hellbender.utils.IGVUtils

public final class IGVUtils
extends java.lang.Object

Utilities for interacting with IGV-specific formats. See https://software.broadinstitute.org/software/igv/

Method Summary

Modifier and Type	Method and Description
static void	printIGVFormatHeader(java.io.PrintStream out, java.lang.String graphType, java.lang.String... columns) Prints a header for an IGV-format file.
static void	printIGVFormatRow(java.io.PrintStream out, htsjdk.samtools.util.Locatable loc, java.lang.String featureName, double... values) Prints a row in an IGV-format file.

Methods inherited from class java.lang.Object

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

Method Detail

printIGVFormatHeader

public static void printIGVFormatHeader(java.io.PrintStream out,
                                        java.lang.String graphType,
                                        java.lang.String... columns)

Prints a header for an IGV-format file. See https://software.broadinstitute.org/software/igv/IGV for details of this format.

Parameters:

out - stream to print the header to

graphType - type of graph (eg., "line")

columns - Column labels for the 5th and subsequent columns, representing the individual "tracks" in the IGV file. Note that the first 4 column labels in an IGV file are required to be Chromosome/Start/End/Feature, and should NOT be passed in here.

printIGVFormatRow

public static void printIGVFormatRow(java.io.PrintStream out,
                                     htsjdk.samtools.util.Locatable loc,
                                     java.lang.String featureName,
                                     double... values)

Prints a row in an IGV-format file. See https://software.broadinstitute.org/software/igv/IGV for details of this format.

Parameters:

out - stream to print the row to

loc - genome location associated with this row (in 1-based closed form)

featureName - name of the feature associated with this row

values - values for each track, corresponding to the 5th and subsequent column names declared in the header