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root/gclib/gclib/gff.cpp

#	Line 7 | Line 7
7
8		const uint GFF_MAX_LOCUS = 7000000; //longest known gene in human is ~2.2M, UCSC claims a gene for mouse of ~ 3.1 M
9		const uint GFF_MAX_EXON  =   30000; //longest known exon in human is ~11K
10	<	const uint GFF_MAX_INTRON= 6000000;
10	>	const uint GFF_MAX_INTRON= 6000000; //Ensembl shows a >5MB human intron
11		bool gff_show_warnings = false; //global setting, set by GffReader->showWarnings()
12		const int gff_fid_mRNA=0;
13		const int gff_fid_transcript=1;
#	Line 976 | Line 976
976		bool GffReader::addExonFeature(GfoHolder* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr) {
977		bool r=true;
978		if (gffline->strand!=prevgfo->gffobj->strand) {
979	<	if (prevgfo->gffobj->strand=='.') {
980	<	prevgfo->gffobj->strand=gffline->strand;
981	<	}
982	<	else {
983	<	GMessage("GFF Error at %s (%c): exon %d-%d (%c) found on different strand; discarded.\n",
984	<	prevgfo->gffobj->gffID, prevgfo->gffobj->strand,
985	<	gffline->fstart, gffline->fend, gffline->strand, prevgfo->gffobj->getGSeqName());
986	<	//r=false;
987	<	return true; //FIXME: split trans-spliced mRNAs by strand
988	<	}
989	<	}
979	>	//TODO: add support for trans-splicing and even inter-chromosomal fusions
980	>	if (prevgfo->gffobj->strand=='.') {
981	>	prevgfo->gffobj->strand=gffline->strand;
982	>	}
983	>	else {
984	>	GMessage("GFF Error at %s (%c): exon %d-%d (%c) found on different strand; discarded.\n",
985	>	prevgfo->gffobj->gffID, prevgfo->gffobj->strand,
986	>	gffline->fstart, gffline->fend, gffline->strand, prevgfo->gffobj->getGSeqName());
987	>	//r=false;
988	>	return true; //FIXME: split trans-spliced mRNAs by strand
989	>	}
990	>	}
991		int gdist=(gffline->fstart>prevgfo->gffobj->end) ? gffline->fstart-prevgfo->gffobj->end :
992		((gffline->fend<prevgfo->gffobj->start)? prevgfo->gffobj->start-gffline->fend :
993		0 );

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