htslib access (un)compressed offsets, now with newest htslib featuring hts_idx_load3 method.

htslib_idx_load.c

#include <stdio.h>
#include <stdlib.h>

#include <htslib/hts.h>
#include <htslib/bgzf.h>
#include <hts_internal.h>
#include <string.h>
#include <unistd.h>

int main(int argc, char **argv)
{
	hts_idx_t *baifile = NULL;

    baifile = hts_idx_load3("htsnexus_test_NA12878.bam",
							"htsnexus_test_NA12878.bam.bai",
							HTS_FMT_BAI, 0);
}

Makefile

all:
        ${CC} -g -Wall -I. -L. -I../rust-htslib/hts-sys/htslib -L../rust-htslib/hts-sys/htslib -I/usr/local/opt/bzip2/include -I/usr/local/Cellar/curl-openssl/7.68.0/include -I/usr/local/Cellar/xz/5.2.4/include -I/usr/local/opt/zlib/include s3_htslib.c -o s3_htslib -llzma -lz -lbz2 -lhts

clean:
        rm s3_htslib

s3_htslib.c

#include <stdio.h>
#include <stdlib.h>

#include <htslib/hfile.h>
#include <htslib/hts.h>
#include <htslib/sam.h>

#include <string.h>
#include <unistd.h>

//export DYLD_LIBRARY_PATH=/Users/romanvg/dev/umccr/htsget/rust-htslib/hts-sys/htslib

int main(int argc, char **argv)
{
	samFile *fp_in = hts_open(argv[1],"r"); //open bam file
	bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //read header

	printf("%s\n", bamHdr->target_name[1]);
}

On OSX Compile with:

$ make -j4 # for htslib itself
$ export DYLD_LIBRARY_PATH=./htslib
$ gcc -g -Wall -I. -I./htslib/ -L./htslib -I. -L. htsget_read_idx.c -o htsget -lhts && ./htsget

Then, usage be like:

$ aws sso login
$ samtools view -H s3://umccr-research-dev/htsget/htsnexus_test_NA12878.bam
(...) (all header)
$ export DYLD_LIBRARY_PATH=/Users/romanvg/dev/umccr/htsget/rust-htslib/hts-sys/htslib
$ ./s3_htslib s3://umccr-research-dev/htsget/htsnexus_test_NA12878.bam
2