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/*++
Module Name:
Read.cpp
Abstract:
Read class for the SNAP sequencer
Authors:
Bill Bolosky, May, 2012
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "Read.h"
#include "SAM.h"
#include "Error.h"
bool
isAValidAlignmentResult(
AlignmentResult result)
{
return result == NotFound || result == SingleHit || result == MultipleHits || result == UnknownAlignment;
}
void
Read::checkIdMatch(
Read* read0,
Read* read1)
{
if (!readIdsMatch(read0, read1)) {
unsigned n[2] = {min(read0->getIdLength(), 200u), min(read1->getIdLength(), 200u)};
char* p[2] = {(char*) alloca((size_t)n[0] + 1), (char*) alloca((size_t)n[1] + 1)};
memcpy(p[0], read0->getId(), n[0]); p[0][n[0]] = 0;
memcpy(p[1], read1->getId(), n[1]); p[1][n[1]] = 0;
WriteErrorMessage("Unmatched read IDs '%s' and '%s'. Use the -I option to ignore this.\n", p[0], p[1]);
soft_exit(1);
}
}
const unsigned Read::localBufferLength = 3 * MAX_READ_LENGTH;
const unsigned DEFAULT_MIN_READ_LENGTH = 50;
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