Refactor csq code to provide a mini library for GFF parsing

Author: pd3

Makefile

@@ -42,7 +42,7 @@ OBJS     = main.o vcfindex.o tabix.o \
            regidx.o smpl_ilist.o csq.o vcfbuf.o \
            mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o read_consensus.o bam_sample.o \
            vcfsort.o cols.o extsort.o dist.o abuf.o \
-           ccall.o em.o prob1.o kmin.o str_finder.o
+           ccall.o em.o prob1.o kmin.o str_finder.o gff.o
 PLUGIN_OBJS = vcfplugin.o
 
 prefix      = /usr/local
@@ -289,6 +289,7 @@ vcfbuf.o: vcfbuf.c $(htslib_vcf_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(bcf
 abuf.o: abuf.c $(htslib_vcf_h) $(bcftools_h) rbuf.h abuf.h
 extsort.o: extsort.c $(bcftools_h) extsort.h kheap.h
 smpl_ilist.o: smpl_ilist.c $(bcftools_h) $(smpl_ilist_h)
+gff.o: gff.c gff.h regidx.h
 csq.o: csq.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_h) $(htslib_khash_str2int_h) $(htslib_kseq_h) $(htslib_faidx_h) $(bcftools_h) $(filter_h) regidx.h kheap.h $(smpl_ilist_h) rbuf.h
 
 # test programs