modified: README.md

	modified:   src/gtf.c

	modified: Makefile

	modified:   Makefile.debug
	modified:   src/bam_anno.c
	modified:   src/bam_count.c
	modified:   src/bam_pool.c
	modified:   src/bed.c
	modified:   src/bed_anno.c
	modified:   src/gtf.c

	new file: src/bed_flatten.c

	new file:   src/gtf2bed.c

	modified: src/bed_anno.c

	modified: src/gtf.c

	modified:   src/gtf.h

	modified: src/callept.c

	modified: src/bam_anno.c

Update README.md

new function update

add counts2