org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput

Class SimpleTsvOutputRenderer

java.lang.Object

org.broadinstitute.hellbender.tools.funcotator.OutputRenderer

org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput.SimpleTsvOutputRenderer

All Implemented Interfaces:

java.lang.AutoCloseable

public class SimpleTsvOutputRenderer
extends OutputRenderer

This class is very versatile, but as a result, it must do some lazy loading after it receives the first write command. IMPORTANT: If this class is not given any command to write(...), the output file will be empty. This class assumes that funcotation maps will have the same fields regardless of allele. This class makes no attempt to render VariantContext attribues. Any VC attributes must be converted into a Funcotation (and added to the FuncotationMap) before calling write(...). This class will append a funcotation for the locatable data. This will use the field names: LocatableFuncotationCreator.CONTIG_FIELD_NAME, LocatableFuncotationCreator.START_FIELD_NAME, and LocatableFuncotationCreator.END_FIELD_NAME If you want the output file to have locatable data in different fields, make sure the alias file maps these to the preferred field name in the output. Sorting of columns is based on the config file: - Columns from the config file in order as appearing in the config file. - Remaining default, override, and funcotation fields in natural/alphanumberical order (e.g. FIELD1, FIELD2, FIELD10). Note that remaining funcotation fields will not appear when `isWriteFuncotationFieldsNotInConfig` is `false` "Remaining" means fields that did not appear in the config file (as a column name nor as an alias) If this output renderer does not actually render any variants, it will not necessarily have the same columns as when there actually are variants. Please note that `isWriteFuncotationFieldsNotInConfig` = false will have the same column list in these cases, but there are other caveats, since leftover funcotation fields will not be written ever.

Field Summary

Fields inherited from class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer

dataSourceFactories, manualAnnotations, toolVersion

Method Summary

Modifier and Type	Method and Description
void	close() Close the OutputRenderer.
static java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>>	createColumnNameToAliasesMap(java.nio.file.Path configFile) Create key value pairs where the key is the output column name and the value is a list of possible field names, in order of priority.
static SimpleTsvOutputRenderer	createFromFile(java.nio.file.Path outputFilePath, java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForDefaultAnnotations, java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForOverrideAnnotations, java.util.Set<java.lang.String> excludedOutputFields, java.nio.file.Path configPath, java.lang.String toolVersion, boolean isWriteColumnsNotInConfig)
static SimpleTsvOutputRenderer	createFromResource(java.nio.file.Path outputFilePath, java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForDefaultAnnotations, java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForOverrideAnnotations, java.util.Set<java.lang.String> excludedOutputFields, java.nio.file.Path resourcePath, java.lang.String toolVersion, boolean isWriteColumnsNotInConfig) Use when loading the config file from the jar.
void	write(htsjdk.variant.variantcontext.VariantContext variant, FuncotationMap txToFuncotationMap) Write the given variant and txToFuncotationMap to the output file.

Methods inherited from class org.broadinstitute.hellbender.tools.funcotator.OutputRenderer

createFuncotationFromLinkedHashMap, getDataSourceInfoString, getToolVersion

Methods inherited from class java.lang.Object

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

Method Detail

close

public void close()

Description copied from class: OutputRenderer

Close the OutputRenderer.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in class OutputRenderer

write

public void write(htsjdk.variant.variantcontext.VariantContext variant,
                  FuncotationMap txToFuncotationMap)

Description copied from class: OutputRenderer

Write the given variant and txToFuncotationMap to the output file.

Specified by:

write in class OutputRenderer

Parameters:

variant - VariantContext to write to the file.

txToFuncotationMap - FuncotationMap to add to the given variant on output.

createColumnNameToAliasesMap

public static java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>> createColumnNameToAliasesMap(java.nio.file.Path configFile)

Create key value pairs where the key is the output column name and the value is a list of possible field names, in order of priority.

Parameters:

configFile - config file that encodes column_name:alias_1,alias_2 ....

Returns:

mapping of output column names to possible field names in order of priority. Never null

createFromFile

public static SimpleTsvOutputRenderer createFromFile(java.nio.file.Path outputFilePath,
                                                     java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForDefaultAnnotations,
                                                     java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForOverrideAnnotations,
                                                     java.util.Set<java.lang.String> excludedOutputFields,
                                                     java.nio.file.Path configPath,
                                                     java.lang.String toolVersion,
                                                     boolean isWriteColumnsNotInConfig)

Parameters:

outputFilePath - Path to write. Never null

unaccountedForDefaultAnnotations - LinkedHashMap of default annotations that must be added. Never null

unaccountedForOverrideAnnotations - LinkedHashMap of override annotations that must be added. Never null

excludedOutputFields - Set column names that are not to appear in the output file. Use an empty set for no exclusions. Never null

configPath - Configuration file where each key is a column and a comma-separated list of fields acts as a list of possible aliases. Note that the list of the keys is the same order that will be seen in the output.

toolVersion - The version number of the tool used to produce the VCF file. Never null

isWriteColumnsNotInConfig - Whether to write funcotation fields that were present but had no alias, no default value, nor override value.

createFromResource

public static SimpleTsvOutputRenderer createFromResource(java.nio.file.Path outputFilePath,
                                                         java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForDefaultAnnotations,
                                                         java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForOverrideAnnotations,
                                                         java.util.Set<java.lang.String> excludedOutputFields,
                                                         java.nio.file.Path resourcePath,
                                                         java.lang.String toolVersion,
                                                         boolean isWriteColumnsNotInConfig)

Use when loading the config file from the jar. See createFromFile(Path, LinkedHashMap, LinkedHashMap, Set, Path, String, boolean)

Parameters:

outputFilePath - See createFromFile(Path, LinkedHashMap, LinkedHashMap, Set, Path, String, boolean)

unaccountedForDefaultAnnotations - See createFromFile(Path, LinkedHashMap, LinkedHashMap, Set, Path, String, boolean)

unaccountedForOverrideAnnotations - See createFromFile(Path, LinkedHashMap, LinkedHashMap, Set, Path, String, boolean)

excludedOutputFields - See createFromFile(Path, LinkedHashMap, LinkedHashMap, Set, Path, String, boolean)

resourcePath - Configuration file (as a Resource). See createFromFile(Path, LinkedHashMap, LinkedHashMap, Set, Path, String, boolean)

toolVersion - See createFromFile(Path, LinkedHashMap, LinkedHashMap, Set, Path, String, boolean)

isWriteColumnsNotInConfig - Whether to write funcotation fields that were present but had no alias, no default value, nor override value.