BaseUtilities Class Reference

This class contains static utilities for performing basic operations on bases. More...

#include <BaseUtilities.h>

List of all members.

Static Public Member Functions
static bool	isAmbiguous (char base)
	Returns whether or not the specified bases is an indicator for ambiguity.
static bool	areEqual (char base1, char base2)
	Returns whether or not two bases are equal (case insensitive), if one of the bases is '=', the bases are consided to be equal.
static uint8_t	getPhredBaseQuality (char charQuality)
	Get phred base quality from the specified ascii quality.
static char	getAsciiQuality (uint8_t phredQuality)
	Get ascii quality from the specified phred quality.
static void	reverseComplement (std::string &sequence)
Static Public Attributes
static const char	UNKNOWN_QUALITY_CHAR = ' '
	Character used when the quality is unknown.
static const uint8_t	UNKNOWN_QUALITY_INT = 0xFF
	Int value used when the quality is unknown.

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Detailed Description

This class contains static utilities for performing basic operations on bases.

Definition at line 27 of file BaseUtilities.h.

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Member Function Documentation

bool BaseUtilities::areEqual	(	char	base1,
		char	base2
	)			[static]

Returns whether or not two bases are equal (case insensitive), if one of the bases is '=', the bases are consided to be equal.

Definition at line 40 of file BaseUtilities.cpp.

Referenced by SamTags::createMDTag(), SamQuerySeqWithRefIter::getNextMatchMismatch(), SamQuerySeqWithRef::seqWithEquals(), and SamQuerySeqWithRef::seqWithoutEquals().

{
    // If they are the same, return true.
    if(base1 == base2)
    {
        return(true);
    }
    // If one of the bases is '=', return true.
    if((base1 == '=') || (base2 == '='))
    {
        return(true);
    }

    // Check both in upercase.
    if(toupper(base1) == toupper(base2))
    {
        // same in upper case.
        return(true);
    }

    // The bases are different.
    return(false);
}

bool BaseUtilities::isAmbiguous

(

char

base

)

[static]

Returns whether or not the specified bases is an indicator for ambiguity.

Returns:

true if base = 'n' or 'N' or '.'

Definition at line 23 of file BaseUtilities.cpp.

Referenced by SamTags::createMDTag(), SamQuerySeqWithRefIter::getNextMatchMismatch(), and SamQuerySeqWithRef::seqWithEquals().

{
    switch(base)
    {
        case 'N':
        case 'n':
        case '.':
            return(true);
            break;
        default:
            break;
    };

    // Not 'N', 'n', or '.', so return false.
    return(false);
}

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The documentation for this class was generated from the following files:

• general/BaseUtilities.h
• general/BaseUtilities.cpp