Draft: Add WGS read reconstruction for ROI

assigned to @worku005

added 1 commit

• 5f13905c - describe in changelog

Compare with previous version

added 1 commit

• 4b7b4243 - fix for when no reads are used

Compare with previous version

added 1 commit

• 0b39dd66 - implement a start on kmerizing stuff meaningfully for roi extraction

Compare with previous version

added 1 commit

• 44951072 - implemented initial filtering step

Compare with previous version

added 1 commit

• 0dc8d86c - implement min count for matching kmers

Compare with previous version

added 3 commits

• 0dc8d86c...9498a2ff - 2 commits from branch add_gfa_export
• e85ac6b3 - Merge branch 'add_gfa_export' into add_wgs_roi

Compare with previous version

added 1 commit

• ab53eeb0 - some updates from real test

Compare with previous version

added 1 commit

• 09ab67b3 - add error for kmerizing of wgs for roi when k is larger than 63

Compare with previous version

added 1 commit

• 08790cc5 - refactor read reconstruction code

Compare with previous version

added 1 commit

• 05ba2ff1 - fixed parallellisation in read reconstruction

Compare with previous version

added 1 commit

• 1165d6d9 - implement progress bars

Compare with previous version

added 1 commit

• 6365037a - implement binary search to try speeding up kmer search for roi wgs

Compare with previous version

added 1 commit

• 114410b8 - add test to ensure that kmerizing code keeps working

Compare with previous version

added 1 commit

• 0acd1276 - deal correctly with invalid nucleotides by skipping over those kmers

Compare with previous version

added 1 commit

• f73e290c - add statement for future me

Compare with previous version

added 1 commit

• 2f9b239d - add more clever cache, but not yet solved the fastq reading bottleneck

Compare with previous version

added 1 commit

• 1d0e86f8 - increase buffer size to 4GB

Compare with previous version

added 1 commit

• 0b3523c0 - put back to what worked

Compare with previous version

added 1 commit

• 70b905ea - adding fastqreader as test

Compare with previous version