d26bec5e152164d0b3035c41b66353c0efed3de6 angie Mon Feb 25 14:37:56 2013 -0800 Removed outdated comment. diff --git src/lib/annoStreamVcf.c src/lib/annoStreamVcf.c index e0ffee1..2d28e8a 100644 --- src/lib/annoStreamVcf.c +++ src/lib/annoStreamVcf.c @@ -2,32 +2,30 @@ #include "annoStreamVcf.h" #include "vcf.h" struct annoStreamVcf { struct annoStreamer streamer; // Parent class members & methods // Private members struct vcfFile *vcff; // VCF parsed header and file object struct vcfRecord *record; // Current parsed row of VCF (need this for chromEnd) char *asWords[VCF_NUM_COLS]; // Current row of VCF with genotypes squashed for autoSql struct dyString *dyGt; // Scratch space for squashing genotype columns int numCols; // Number of columns in autoSql def of VCF. int numFileCols; // Number of columns in VCF file. boolean isTabix; // True if we are accessing compressed VCF via tabix index -//#*** we need a way to pass the VCF header to the VCF formatter. -//#*** streamer getHeader method?? }; static void asvSetRegion(struct annoStreamer *vSelf, char *chrom, uint regionStart, uint regionEnd) /* Set region -- and free current sqlResult if there is one. */ { annoStreamerSetRegion(vSelf, chrom, regionStart, regionEnd); struct annoStreamVcf *self = (struct annoStreamVcf *)vSelf; if (self->isTabix) lineFileSetTabixRegion(self->vcff->lf, chrom, regionStart, regionEnd); else if (chrom != NULL) errAbort("annoStreamVcf: setRegion not yet implemented for non-tabix VCF."); } static char *asvGetHeader(struct annoStreamer *vSelf)