NAME
CracTools::SAMReader::SAMline - The object for manipulation a SAM line.
VERSION
version 1.251
SYNOPSIS
$sam_line = CracTools::SAMReader::SAMline->new($line);
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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
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Methods
new
Arg [1] : String - SAM line in TAB-separated format.
Example : $sam_line = CracTools::SAMline->new$($line);
Description : Create a new CracTools::SAMline obect.
ReturnType : CracTools::SAMline
Exceptions : none
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isFlagged
Arg [1] : Integer - The flag to test (1,2,4,8, ... ,1024)
Example : if($SAMline->isFlagged($fags{unmapped}) {
DO_SOMETHING...
};
Description : Test if the line has the flag in parameter setted.
ReturnType : Boolean
Exceptions : none
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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
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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.
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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
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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
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GETTERS AND SETTERS
line
Description : Getter for the whole SAMline as a string.
ReturnType : String
Exceptions : none
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updatedLine
Description : Getter/Setter for the updated line.
If there is not updated line, this method return
the original SAM line.
RetrunType : String
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qname
Description : Getter/Setter for attribute qname
ReturnType : String
Exceptions : none
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flag
Description : Getter/Setter for attribute flag
ReturnType : String
Exceptions : none
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rname
Description : Getter/Setter for attribute rname (chromosome for eucaryotes)
ReturnType : String
Exceptions : none
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chr
Description : Getter/Setter for attribute rname (Alias)
ReturnType : String
Exceptions : none
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pos
Description : Getter/Setter for attribute pos (position of the sequence)
ReturnType : String
Exceptions : none
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mapq
Description : Getter/Setter for attribute mapq (mapping quality)
ReturnType : String
Exceptions : none
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cigar
Description : Getter/Setter for attribute cigar (see SAM doc)
ReturnType : String
Exceptions : none
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rnext
Description : Getter/Setter for attribute rnext (see SAM doc)
ReturnType : String
Exceptions : none
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pnext
Description : Getter/Setter for attribute pnext (see SAM doc)
ReturnType : Integer
Exceptions : none
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tlen
Description : Getter/Setter for attribute tlen (sequence length)
ReturnType : Integer
Exceptions : none
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seq
Description : Getter/Setter for attribute seq (the sequence).
sequence, that what you need in most cases.
ReturnType : String
Exceptions : none
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qual
Description : Getter/Setter for attribute qual (sequence quality)
ReturnType : String
Exceptions : none
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getOptionalField
Example :
Description :
ReturnType :
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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
]
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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
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pSupport
Description : Return the support profile of the read if the SAM file has been generated with
CRAC option --detailed
ReturnType : String
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pLoc
Description : Return the location profile of the read if the SAM file has been generated with
CRAC option --detailed
ReturnType : String
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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
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isPairedClassified
Arg [1] : String - The class to test :
- "unique"
- "duplicated"
- "multiple"
Description : Test paired-end read clasification
ReturnType : Boolean
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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 :
$read->genericInfo("foo","bar")
print $read->genericInfo("foo");
ReturnType : ?
Exceptions : none
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isClassified
Arg [1] : String - The class to test :
- "unique"
- "duplicated"
- "multiple"
- "normal"
- "almostNormal"
Example : if($sam_line->isClassified('normal')) {
DO_SOMETHING;
}
Description : Test if the line is classified according to the parameter value.
ReturnType : Boolean
Exceptions : none
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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
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PRIVATE METHODS
loadEvents
Example : $sam_line->loadEvents();
Description : Loading of events attributes
ReturnType : none
Exceptions : none
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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
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removeEvent
Arg [1] : Hash reference - The event object
Description : Remove the event from the event hash and from the line.
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updateEvent
loadSamDetailed
Example : $sam_line->loadSamDetailed();
Description : Loading of sam detaileds attributes
ReturnType : none
Exceptions : none
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loadPaired
Example : $sam_line->loadPaired();
Description : Loading of sam detaileds attributes
ReturnType : none
Exceptions : none
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expandCracLoc
Arg [1] : String - Localisation in crac format : Chromosome|strand,position
Ex : X|-1,2332377
Description : Extract Chromosme, position and strand as separated variable from
the localisation in CRAC format.
ReturnType : Array($chromosome,$position,$strand)
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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)
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AUTHORS
Nicolas PHILIPPE <nphilippe.research@gmail.com>
Jérôme AUDOUX <jaudoux@cpan.org>
Sacha BEAUMEUNIER <sacha.beaumeunier@gmail.com>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2017 by IRMB/INSERM (Institute for Regenerative Medecine and Biotherapy / Institut National de la Santé et de la Recherche Médicale) and AxLR/SATT (Lanquedoc Roussilon / Societe d'Acceleration de Transfert de Technologie).
This is free software, licensed under:
The GNU Affero General Public License, Version 3, November 2007
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