## Samtools has a hard coded maximum number of 
## alignments that pileup will return.
##
## We have increased that limit.

htslib/sam.c:
< 	iter->maxcnt = 8000;
---
> 	iter->maxcnt = 1000000000;


bamtk.c
Comment out main function

Copy Makefile to Makefile.original

Makefile:
# Build extra code into this library
libbam.a:$(LOBJS) $(AOBJS)
	$(AR) -csru $@ $(LOBJS) $(AOBJS)

Move lib:libbam.a to top of makefile



$(LIBBAM)


libhts/Makefile:
Move to top of makefile
lib-static: libhts.a

libhts/bam_import.c
#comment out error printing
//fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", n_targets);