#
# Use .add_data_files and .add_data_dir methods in a appropriate
# setup.py files to include non-python files such as documentation,
# data, etc files to distribution. Avoid using MANIFEST.in for that.
#
include MANIFEST.in
include COPYING
include INSTALL
include KNOWN_BUGS
include THANKS
include cy_build.py
include requirements.txt
include pysam/c*.pxd
include pysam/c*.pyx
include pysam/c*.c
include pysam/*.c
include pysam/*.h
include samtools/configure
include samtools/config.mk.in
include samtools/config.h.in
include samtools/*.h
exclude samtools/config.h
include samtools/*/*.h
include htslib/*.c
include htslib/*.h
exclude htslib/config.h
include htslib/Makefile
include htslib/htslib_vars.mk
include htslib/configure
include htslib/config.mk.in
include htslib/config.h.in
include htslib/htslib/*.h
include htslib/cram/*.c
include htslib/cram/*.h
include cy_build.py
include pysam.py
include requirements.txt

# pysam tests
include tests/00README.txt
include tests/pysam_data
include tests/tabix_data
include tests/*.py
#ex1.fa
#include tests/ex1.sam.gz
#include tests/ex3.sam
#include tests/ex4.sam
#include tests/ex5.sam
#include tests/ex6.sam
#include tests/ex7.sam
#include tests/ex8.sam
#include tests/ex9_fail.bam
#include tests/ex9_nofail.bam
#include tests/ex10.sam
#include tests/example.py
#include tests/pysam_test.py
#include tests/segfault_tests.py
#include tests/example_*.sam
#include tests/example_btag.bam
#include tests/tag_bug.bam
#include tests/example.vcf40
#include tests/example_empty_header.bam
#include tests/test_unaligned.bam
#include tests/issue100.bam

# tabix tests
#include tests/example.gtf.gz
#include tests/example.gtf.gz.tbi
#include tests/example.bed.gz
#include tests/example.bed.gz.tbi
#include tests/vcf-examples/*.vcf

# documentation
include doc/*