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 / 
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".