-
Notifications
You must be signed in to change notification settings - Fork 60
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Support plaintext fasta on desktop by dynamically creating a FAI file on the fly #2443
Conversation
c90e963
to
9b96f76
Compare
Codecov Report
@@ Coverage Diff @@
## main #2443 +/- ##
==========================================
- Coverage 61.16% 61.11% -0.06%
==========================================
Files 540 540
Lines 25147 25168 +21
Branches 5873 5881 +8
==========================================
Hits 15381 15381
- Misses 9445 9466 +21
Partials 321 321
Continue to review full report at Codecov.
|
9b96f76
to
1aa3269
Compare
have you tested the error handling for when the index generator fails? |
1aa3269
to
f40decb
Compare
should be ok, it has a little error display if no sequences were found in the file for example (staying at the OpenSequenceDialog screen) |
1272b67
to
8a9a9dc
Compare
had a limitation before that only allowed fasta with \n and not \r\n but now allows both |
8a9a9dc
to
31fa4c9
Compare
Add split2 to fasta Updates Split on \n only to allow \r to be used in byte offset calculations
2703581
to
c02712e
Compare
Fixes #2428
Allows streaming a large FASTA file so the operation remains out of memory, creates a FAI file on the fly, stores it in userData/fai/filename+Date.now()+.fai and then dynamically creates an IndexedFastaAdapter config from this
Helps aid memory usage so that we don't have to load the whole genome into memory
Uses some of the concepts learned about streaming files from text-index in the process