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#include "piler2.h"
static void WriteCrisp(FILE *f, const PileData &Pile, int PileIndex)
{
int FamIndex = Pile.FamIndex;
assert(FamIndex >= 0);
int ContigFrom;
const char *ContigLabel = GlobalToContig(Pile.From, &ContigFrom);
const int Length = Pile.To - Pile.From + 1;
const int ContigTo = ContigFrom + Length - 1;
const char Strand = Pile.Rev ? '-' : '+';
// GFF fields are:
// <seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]
// 0 1 2 3 4 5 6 7 8 9
fprintf(f, "%s\tpiler\ttrs\t%d\t%d\t0\t%c\t.\tFamily %d ; Pile %d\n",
ContigLabel,
ContigFrom + 1,
ContigTo + 1,
Strand,
FamIndex,
PileIndex);
}
void WriteCrispFile(const char *OutputFileName, const PileData *Piles, int PileCount)
{
FILE *f = OpenStdioFile(OutputFileName, FILEIO_MODE_WriteOnly);
for (int PileIndex = 0; PileIndex < PileCount; ++PileIndex)
{
const PileData &Pile = Piles[PileIndex];
if (-1 == Pile.FamIndex)
continue;
WriteCrisp(f, Pile, PileIndex);
}
fclose(f);
}
void WriteArray(FILE *f, int FamIndex, int Lo, int Hi)
{
assert(FamIndex >= 0);
int ContigFrom;
const char *ContigLabel = GlobalToContig(Lo, &ContigFrom);
const int Length = Hi - Lo + 1;
const int ContigTo = ContigFrom + Length - 1;
const char Strand = '+';
// GFF fields are:
// <seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]
// 0 1 2 3 4 5 6 7 8 9
fprintf(f, "%s\tpiler\ttrs\t%d\t%d\t0\t%c\t.\tFamily %d\n",
ContigLabel,
ContigFrom + 1,
ContigTo + 1,
Strand,
FamIndex);
}
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