/ 
CracTools-core-1.03
/ CracTools::SAMReader::SAMline

NAME

CracTools::SAMReader::SAMline - The object for manipulation a SAM line.

SYNOPSIS

use CracTools::SAMReader::SAMline;

$sam_line = CracTools::SAMReader::SAMline->new($line);

DESCRIPTION

An object for easy acces to SAM line fields. See SAM Specifications for more informations : http://samtools.sourceforge.net/SAM1.pdf

Variables

%flags

SAM flags :

  • MULTIPLE_SEGMENTS => 1

  • PROPERLY_ALIGNED => 2

  • UNMAPPED => 4,

  • NEXT_UNMAPPED => 8,

  • REVERSE_COMPLEMENTED => 16,

  • NEXT_REVERSE_COMPLEMENTED => 32,

  • FIRST_SEGMENT => 64,

  • LAST_SEGMENT => 128,

  • SECONDARY_ALIGNMENT => 256,

  • QUALITY_CONTROLS_FAILED => 512,

  • PCR_DUPLICATED => 1024,

  • CHIMERIC_ALIGNMENT => 2048,

STATIC PARSING METHODS

These methods can be used without creating an CracTools::SAMReader::SAMline object. They are designed to provided efficient performance when parsing huge SAM files, because creating object in Perl can be long and useless for some purposes.

hasEvent

Arg [1] : String - SAM line
Arg [2] : eventType

Methods

new

Arg [1] : String - SAM line in TAB-separated format.

Example     : $sam_line = CracTools::SAMline->new$($line);
Description : Create a new CracTools::SAMline obect.
ReturnType  : CracTools::SAMline
Exceptions  : none

isFlagged

Arg [1] : Integer - The flag to test (1,2,4,8, ... ,1024)

Example     : if($SAMline->isFlagged($fags{unmapped}) {
                DO_SOMETHING... 
              };
Description : Test if the line has the flag in parameter setted.
ReturnType  : Boolean
Exceptions  : none

getStrand

Example     : $strand = $SAMline->getStrand(); 
Description : Return the strand of the SAMline :
              - "1" if forward strand
              - "-1" if reverse strand
ReturnType  : 1 or -1
Exceptions  : none

getOriginalSeq

Descrition   : Return the original sequence as it was in the FASTQ file.
               In fact we reverse complemente the sequence if flag 16 is raised.

getLocAsCracFormat

Example     : $loc = $SAMline->getLocAsCracFormat(); 
Description : Return the location of the sequence using CRAC format : "chr|strand,position".
              For example : X|-1,2154520
ReturnType  : String
Exceptions  : none

getPatch

Description : If the SAMline has been modified, this method will generate
              a patch in UnifiedDiff format that represent the changes.
ReturnType  : String (patch) if line has changed, False (0) either.
Exceptions  : none

GETTERS AND SETTERS

line

Description : Getterr for the whole SAMline as a string.
ReturnType  : String
Exceptions  : none

updatedLine

Description : Getter/Setter for the updated line.
              If there is not updated line, this method return
              the original SAM line.
RetrunType  : String

qname

Description : Getter/Setter for attribute qname
ReturnType  : String
Exceptions  : none

flag

Description : Getter/Setter for attribute flag
ReturnType  : String
Exceptions  : none

rname

Description : Getter/Setter for attribute rname (chromosome for eucaryotes)
ReturnType  : String
Exceptions  : none

chr

Description : Getter/Setter for attribute rname (Alias)
ReturnType  : String
Exceptions  : none

pos

Description : Getter/Setter for attribute pos (position of the sequence)
ReturnType  : String
Exceptions  : none

mapq

Description : Getter/Setter for attribute mapq (mapping quality)
ReturnType  : String
Exceptions  : none

cigar

Description : Getter/Setter for attribute cigar (see SAM doc)
ReturnType  : String
Exceptions  : none

rnext

Description : Getter/Setter for attribute rnext (see SAM doc)
ReturnType  : String
Exceptions  : none

pnext

Description : Getter/Setter for attribute pnext (see SAM doc)
ReturnType  : Integer
Exceptions  : none

tlen

Description : Getter/Setter for attribute tlen (sequence length)
ReturnType  : Integer
Exceptions  : none

seq

Description : Getter/Setter for attribute seq (the sequence).
              Please use getOriginalSeq if you want to retrieve the oriented
              sequence, that what you need in most cases.
ReturnType  : String
Exceptions  : none

qual

Description : Getter/Setter for attribute qual (sequence quality)
ReturnType  : String
Exceptions  : none

getOptionalField

Example     : 
Description : 
ReturnType  :

getChimericAlignments

Description : Parser of SA fields of SAM file in order to find chimeric reads
ReturnType  : Array reference
              Elements are hash [ chr    => String, 
                                  pos    => int, 
                                  strand => 1/-1, 
                                  cigar  => String,
                                  mapq   => int,
                                  edist  => int
                                ]

getCigarOperatorsCount

Example     : my %cigar_counts = %{ $sam_line->getCigarOperatorsCount() };
              print "nb mismatches; ",$cigar_counts{X},"\n";
Description : Return a hash reference where the keys are the cigar operators and the values
              the sum of length associated for each operator.
              For cigar 5S3M1X2M10S, getCigarOperatorsCounts() will retrun :
              { 'S' => 15,
                'M' => 5,
                'X' => 1,
              };
ReturnType  : Hash reference

pSupport

Description : Return the support profile of the read if the SAM file has been generated with
              CRAC option --detailed
ReturnType  : String

pLoc

Description : Return the location profile of the read if the SAM file has been generated with
              CRAC option --detailed
ReturnType  : String

pairedChimera

Description : return the chimeric coordinates of the paired chimera associated to this read if there is one

ReturnType  : array(chr1,pos1,strand1,chr2,pos2,strand2) or undef

isPairedClassified

Arg [1] : String - The class to test :
          - "unique"
          - "duplicated"
          - "multiple"

Description : Test paired-end read clasification

ReturnType  : Boolean

genericInfo

[1] : Key of the generic info
[2] : (Optional) Value of the generic info

Description : Getter/Setter enable to store additional (generic) information 
              about the SAMline as a Key/Value. 
Example : # Set a generic info
          $read->genericInfo("foo","bar")

          # Get a generic info
          print $read->genericInfo("foo"); # this will print "bar"
ReturnType : ?
Exceptions : none

isClassified

Arg [1] : String - The class to test :
          - "unique"
          - "duplicated"
          - "multiple"
          - "normal"
          - "almostNormal"

Example     : if($sam_line->isClassified('normal')) {
                DO_SOMETHING;
              }
Description : Test if the line is classified according to the parameter value.
ReturnType  : Boolean
Exceptions  : none

events

Arg [1] : String - The event type to return :
          - Junction
          - Ins
          - Del
          - SNP
          - Error
          - Chimera
          - Undetermined
          - BioUndetermined
          - ... (see CRAC SAM format specifications for more informations).
Example     : my @junctions = @{$line->events('Junction')};
              foreach my $junction (@junctions) {
                print "Foud Junction : [type : $junction->{type}, loc : $junction->{loc}, gap : $junction->{gap}]\n";
              } 
Description : Return all events of the type specified in parameter
ReturnType  : Array reference
Exceptions  : none

PRIVATE METHODS

loadEvents

Example     : $sam_line->loadEvents();
Description : Loading of events attributes
ReturnType  : none
Exceptions  : none

addEvent

Arg [1] : String - The event type
Arg [2] : Hash reference - The event object
Example     : $line->addEvent($event_type,\%event); 
Description : Return all events of the type specified in parameter
ReturnType  : none
Exceptions  : none

removeEvent

Arg [1] : Hash reference - The event object

Description : Remove the event from the event hash and from the line.

updateEvent

loadSamDetailed

Example     : $sam_line->loadSamDetailed();
Description : Loading of sam detaileds attributes
ReturnType  : none
Exceptions  : none

loadPaired

Example     : $sam_line->loadPaired();
Description : Loading of sam detaileds attributes
ReturnType  : none
Exceptions  : none

expandCracLoc

Arg [1] : String - Localisation in crac format : Chromosome|strand,position
          Ex : X|-1,2332377

Description : Extract Chromosme, position and strand as separated variable from
              the localisation in CRAC format.
ReturnType  : Array($chromosome,$position,$strand)

compressCracLoc

Arg [1] : String - Chromosome
Arg [2] : Integer - Postition
Arg [3] : Integer (1,-1) - Strand

Description : Reverse function of "expandCracLoc"
ReturnType  : String (localisation in CRAC format)

AUTHORS

Jerome AUDOUX <jerome.audoux@etud.univ-montp2.fr>.

COPYRIGHT AND LICENSE

Copyright (C) 2012-2013 -- IRB/INSERM (Institut de Recherche en Biothérapie / Institut National de la Santé et de la Recherche Médicale) LIRMM/UM2 (Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier / Université de Montpellier 2)

FRENCH

Ce fichier fait partie du Pipeline de traitement de données NGS de la plateforme ATGC labélisée par le GiS IBiSA.

Ce logiciel est régi par la licence CeCILL soumise au droit français et respectant les principes de diffusion des logiciels libres. Vous pouvez utiliser, modifier et/ou redistribuer ce programme sous les conditions de la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur le site "http://www.cecill.info".

ENGLISH

This File is part of the NGS data processing Pipeline of the ATGC accredited by the IBiSA GiS.

This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".