.dockerignore

**/.classpath
**/.dockerignore
**/.env
**/.git
**/.gitignore
**/.project
**/.settings
**/.toolstarget
**/.vs
**/.vscode
**/*.*proj.user
**/*.dbmdl
**/*.jfm
**/bin
**/charts
**/docker-compose*
**/compose*
**/Dockerfile*
**/node_modules
**/npm-debug.log
**/obj
**/secrets.dev.yaml
**/values.dev.yaml
README.md

MacOS-related
*.DS_Store
*/*.DS_Store

#Ignoring result directories
**/test/data/*/
**/test/data/*.tar.gz
**/test/blasr/*/
**/test/blend/*/
**/test/conlsh/*/
**/test/lra/*/
**/test/mhap/*/
**/test/minimap2/*/
**/test/winnowmap/*/
**/test/strobealign/*/

**/test/comparisons/*/read_mapping/*mosdepth*
**/test/comparisons/*/read_mapping/*per-base*
**/test/comparisons/*/read_mapping/*.breadth
**/test/comparisons/*/read_mapping/*.samtools.*
**/test/comparisons/*/read_mapping/*.bam*.bed
**/test/comparisons/*/read_mapping/*.stats
**/test/comparisons/*/read_mapping/*.mapeval
**/test/comparisons/*/read_mapping/*.csv
**/test/comparisons/*/read_mapping/*.npz
**/test/comparisons/*/read_mapping/*.tab
**/test/comparisons/*/read_mapping/figures/

**/test/comparisons/*/overlap/quast/
**/test/comparisons/*/overlap/dnadiff/
**/test/comparisons/*/overlap/*.stats
**/test/comparisons/*/overlap/*.ov-eval
**/test/comparisons/*/overlap/figures/

**/test/comparisons/*/sv_calling/*/
**/test/comparisons/*/sv_calling/*.err
**/test/comparisons/*/sv_calling/*.out

**/test/figures/fuzzy_seed_matching/blend*.csv
**/test/figures/fuzzy_seed_matching/minimap2*.csv
**/test/figures/fuzzy_seed_matching/minimap2*.csv
**/test/figures/fuzzy_seed_matching/*.fasta
**/test/figures/fuzzy_seed_matching/aligned_kmers/*.fasta
**/test/figures/fuzzy_seed_matching/*_collision_stats.txt

**/test/figures/*/*/*.pdf
**/test/figures/*/*/*.eps
**/test/figures/*/*.pdf
**/test/mhap/*.out
**/test/mhap/*.err