Uses of Class
org.seqdoop.hadoop_bam.SAMFormat

Packages that use SAMFormat

Package	Description
org.seqdoop.hadoop_bam
org.seqdoop.hadoop_bam.cli
org.seqdoop.hadoop_bam.util

Uses of SAMFormat in org.seqdoop.hadoop_bam

Fields in org.seqdoop.hadoop_bam declared as SAMFormat

Modifier and Type	Field and Description
protected SAMFormat	AnySAMOutputFormat.format

Methods in org.seqdoop.hadoop_bam that return SAMFormat

Modifier and Type	Method and Description
SAMFormat	AnySAMInputFormat.getFormat(org.apache.hadoop.fs.Path path) Returns the SAMFormat corresponding to the given path.
static SAMFormat	SAMFormat.inferFromData(InputStream in)
static SAMFormat	SAMFormat.inferFromFilePath(org.apache.hadoop.fs.Path path) Infers the SAM format by looking at the filename of the given path.
static SAMFormat	SAMFormat.inferFromFilePath(String name) Infers the SAM format by looking at the extension of the given file name.
static SAMFormat	SAMFormat.valueOf(String name) Returns the enum constant of this type with the specified name.
static SAMFormat[]	SAMFormat.values() Returns an array containing the constants of this enum type, in the order they are declared.

Constructors in org.seqdoop.hadoop_bam with parameters of type SAMFormat

Constructor and Description
AnySAMOutputFormat(SAMFormat fmt) Creates a new output format for the given SAM format.
KeyIgnoringAnySAMOutputFormat(SAMFormat fmt)

Constructor parameters in org.seqdoop.hadoop_bam with type arguments of type SAMFormat

Constructor and Description
AnySAMInputFormat(Map<org.apache.hadoop.fs.Path,SAMFormat> formatMap) Creates a new input format, trusting the given Map to define the file-to-format associations.

Uses of SAMFormat in org.seqdoop.hadoop_bam.cli

Fields in org.seqdoop.hadoop_bam.cli declared as SAMFormat

Modifier and Type	Field and Description
protected SAMFormat	CLIMRBAMPlugin.samFormat

Methods in org.seqdoop.hadoop_bam.cli with parameters of type SAMFormat

Modifier and Type	Method and Description
static void	Utils.mergeSAMInto(org.apache.hadoop.fs.Path out, org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, SAMFormat format, org.apache.hadoop.conf.Configuration conf, String commandName) Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header.

Uses of SAMFormat in org.seqdoop.hadoop_bam.util

Methods in org.seqdoop.hadoop_bam.util with parameters of type SAMFormat

Modifier and Type	Method and Description
OutputStream	SAMOutputPreparer.prepareForRecords(OutputStream out, SAMFormat format, htsjdk.samtools.SAMFileHeader header) Prepares the given output stream for writing of SAMRecords in the given format.