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/*++
Module Name:
FASTA.h
Abstract:
FASTA reader
Authors:
Bill Bolosky, August, 2011
Environment:
User mode service.
Revision History:
Adapted from Matei Zaharia's Scala implementation.
--*/
#pragma once
#include "Genome.h"
//
// There are several ways of specifying ALT contigs. There is an opt-in list of ALTs, an opt-out list of regular chromosomes (these must be mutually
// exclusive), and a size cutoff below which is contig is an ALT. The opt-in and opt-out lists supersede the size cutoff.
//
const Genome *
ReadFASTAGenome(
const char *fileName,
const char *pieceNameTerminatorCharacters,
bool spaceIsAPieceNameTerminator,
unsigned chromosomePaddingSize,
const char* const*opt_in_alt_names,
int opt_in_alt_names_count,
const char* const*opt_out_alt_names,
int opt_out_alt_names_count,
GenomeDistance maxSizeForAutomaticALT,
bool autoAlt);
//
// The FASTA appending functions return whether the write was successful.
//
// WARNING: They write very long lines.
// According to Wikipedia, a FASTA file's line limit should be 120, or better, 79.
// Unix workaround if the piece names aren't too long: 'fold -w 79'.
//
bool
AppendFASTAGenome(const Genome *, FILE *fasta);
//
// This is arbitrary; is there some existing convention?
//
inline const char *diploidFASTASexPrefix(bool male)
{
return male ? "PATERNAL|" : "MATERNAL|";
}
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