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#include "piler2.h"
void Annot()
{
const char *InputFileName = RequiredValueOpt("annot");
const char *RepeatFileName = RequiredValueOpt("rep");
const char *OutputFileName = RequiredValueOpt("out");
ProgressStart("Reading repeat file");
int RepCount;
RepData *Reps = ReadReps(RepeatFileName, &RepCount);
ProgressDone();
Progress("%d records", RepCount);
FILE *fInput = OpenStdioFile(InputFileName);
FILE *fOutput = OpenStdioFile(OutputFileName, FILEIO_MODE_WriteOnly);
ProgressStart("Transferring annotation");
GFFRecord Rec;
while (GetNextGFFRecord(fInput, Rec))
{
const bool Rev = Rec.Strand == '-';
const char *Annot = MakeAnnot(Rec.SeqName, Rec.Start-1, Rec.End-1, Rev,
Reps, RepCount);
fprintf(fOutput, "%s\t%s\t%s\t%d\t%d\t%.3g\t%c",
// 0 1 2 3 4 5 6
Rec.SeqName, // 0
Rec.Source, // 1
Rec.Feature, // 2
Rec.Start, // 3
Rec.End, // 4
Rec.Score, // 5
Rec.Strand); // 6
if (-1 == Rec.Frame)
fprintf(fOutput, "\t.");
else
fprintf(fOutput, "\t%d", Rec.Frame);
fprintf(fOutput, "\t%s ; Annot \"%s\"\n", Rec.Attrs, Annot);
}
fclose(fInput);
fclose(fOutput);
ProgressDone();
}
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