.gitignore

**/target
**/*.rs.bk
*.fa*
*.ans
*.sam
**/last
*.maf
*.dat
**/result
**/data
**/logfiles
**/pdf
**/png
**/pics
script/*.sh
script/*.job
script/*.yml
script/sync_*
!.gitignore
venv
**__pycache__*
python/build
python/dist
python/jtk_definitions.egg-info
*~
*.ipynb
!script/alntv_prepare.sh
!script/phase_by_longphase.sh
!script/extract_cox_pgf.sh
!script/phase_mock_reads_from_mock_genome_baseline.sh
!script/phase_mock_reads_from_mhc_baseline.sh
!script/phase_mock_reads_from_mock_genome.sh
!script/phase_mock_reads_from_mhc.sh
!script/phasing_w_reference.sh
!script/pipeline.sh
!script/rename_fastq.awk
!script/var_check.rs
!script/map_hg002.sh
!script/generate_mock_reads_from_mock_genome.sh
!script/generate_mock_reads_from_mhc.sh
!script/extract_cox_pgf.sh
!script/benchmark_clustering.sh
!script/benchmark_mcmc.sh
!script/see_metric.sh