picard.sam.util

Class ReadNameParser

java.lang.Object

picard.sam.util.ReadNameParser

Direct Known Subclasses:

OpticalDuplicateFinder

public class ReadNameParser
extends java.lang.Object

Provides access to the physical location information about a cluster. All values should be defaulted to -1 if unavailable. ReadGroup and Tile should only allow non-zero positive integers, x and y coordinates may be negative.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT_READ_NAME_REGEX The read name regular expression (regex) is used to extract three pieces of information from the read name: tile, x location, and y location.

Constructor Summary

Constructors

Constructor and Description
ReadNameParser() Creates are read name parser using the default read name regex and optical duplicate distance.
ReadNameParser(java.lang.String readNameRegex) Creates are read name parser using the given read name regex.
ReadNameParser(java.lang.String readNameRegex, htsjdk.samtools.util.Log log) Creates are read name parser using the given read name regex.

Method Summary

Modifier and Type	Method and Description
boolean	addLocationInformation(java.lang.String readName, PhysicalLocation loc) Method used to extract tile/x/y from the read name and add it to the PhysicalLocationShort so that it can be used later to determine optical duplication
static int	getLastThreeFields(java.lang.String readName, char delim, int[] tokens) Given a string, splits the string by the delimiter, and returns the the last three fields parsed as integers.
static int	rapidParseInt(java.lang.String input) Very specialized method to rapidly parse a sequence of digits from a String up until the first non-digit character.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_READ_NAME_REGEX

public static final java.lang.String DEFAULT_READ_NAME_REGEX

The read name regular expression (regex) is used to extract three pieces of information from the read name: tile, x location, and y location. Any read name regex should parse the read name to produce these and only these values. An example regex is: (?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*$ which assumes that fields in the read name are delimited by ':' and the last three fields correspond to the tile, x and y locations, ignoring any trailing non-digit characters. The default regex is optimized for fast parsing (see getLastThreeFields(String, char, int[])) by searching for the last three fields, ignoring any trailing non-digit characters, assuming the delimiter ':'. This should consider correctly read names where we have 5 or 7 field with the last three fields being tile/x/y, as is the case for the majority of read names produced by Illumina technology.

Constructor Detail

ReadNameParser

public ReadNameParser()

Creates are read name parser using the default read name regex and optical duplicate distance. See DEFAULT_READ_NAME_REGEX for an explanation on how the read name is parsed.

ReadNameParser

public ReadNameParser(java.lang.String readNameRegex)

Creates are read name parser using the given read name regex. See DEFAULT_READ_NAME_REGEX for an explanation on how to format the regular expression (regex) string.

Parameters:

readNameRegex - the read name regular expression string to parse read names, null to never parse location information.

ReadNameParser

public ReadNameParser(java.lang.String readNameRegex,
                      htsjdk.samtools.util.Log log)

Creates are read name parser using the given read name regex. See DEFAULT_READ_NAME_REGEX for an explanation on how to format the regular expression (regex) string.

Parameters:

readNameRegex - the read name regular expression string to parse read names, null to never parse location information..

log - the log to which to write messages.

Method Detail

addLocationInformation

public boolean addLocationInformation(java.lang.String readName,
                                      PhysicalLocation loc)

Method used to extract tile/x/y from the read name and add it to the PhysicalLocationShort so that it can be used later to determine optical duplication

Parameters:

readName - the name of the read/cluster

loc - the object to add tile/x/y to

Returns:

true if the read name contained the information in parsable form, false otherwise

getLastThreeFields

public static int getLastThreeFields(java.lang.String readName,
                                     char delim,
                                     int[] tokens)
                              throws java.lang.NumberFormatException

Given a string, splits the string by the delimiter, and returns the the last three fields parsed as integers. Parsing a field considers only a sequence of digits up until the first non-digit character. The three values are stored in the passed-in array.

Throws:

java.lang.NumberFormatException - if any of the tokens that should contain numbers do not start with parsable numbers

rapidParseInt

public static int rapidParseInt(java.lang.String input)
                         throws java.lang.NumberFormatException

Very specialized method to rapidly parse a sequence of digits from a String up until the first non-digit character.

Throws:

java.lang.NumberFormatException - if the String does not start with an optional - followed by at least on digit