Skip to content
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.

Sign up for GitHub

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

Jump to bottom

Fixed for 3.4 #172

Merged
merged 43 commits into from
Apr 16, 2024
Merged

Fixed for 3.4 #172

merged 43 commits into from
Apr 16, 2024

Conversation

andrewprzh
Copy link
Collaborator

a lot of minor fixes and improvements:

  • GTF checks
  • gzipping large output (todo: add to manual)
  • reassign reads after filtering
  • print lib versions
  • fix extended annotation missing genes
  • BAM files stats

@andrewprzh andrewprzh requested a review from almiheenko April 11, 2024 13:44
andrewprzh added 29 commits April 11, 2024 17:41
@andrewprzh
refactor model printer
bb9cc13
@andrewprzh
move old file
d9a305f
@andrewprzh
proper extended transcript printer
2327cd7
@andrewprzh
canonical fix
f7adcc9
@andrewprzh
factor out canonical checks
eefb03c
@andrewprzh
bam stats
73c9c71
@andrewprzh
remove old storage
b5ff31d
@andrewprzh
add proper stats to count files
d46ec68
@andrewprzh
fix unassigned
89917ef
@andrewprzh
log versions
9f88772
@andrewprzh
fix test for different minimap version
ac4a129
@andrewprzh
fix extended gtf for empty chromosomes
4a05f34
@andrewprzh
fix --resume
270e503
@andrewprzh
reassign reads after filtering
40916b8
@andrewprzh
do not count reads twice
ca6b93f
@andrewprzh
fix nogtf
8aaf575
@andrewprzh
fix naming
eda73ba
@andrewprzh
use set
ceb037a
@andrewprzh
pyfasta version
09f4416
@andrewprzh
correctly reassign reads after transcript filtering
a46a75f
@andrewprzh
properly count models after the assignment
fe3bd23
@andrewprzh
remove badge
229cbaf
@andrewprzh
gzipped option, compress large files by default
c300bbf
@andrewprzh
introduce GTF check
64e06bd
@andrewprzh
allow gzipped annotations
816d9dd
@andrewprzh
fix console tests
9607888
@andrewprzh
add log message
87e9868
@andrewprzh
do not check GTF is .db already exists
a01beb6
@andrewprzh
fix temporary assert
39b0242
@andrewprzh andrewprzh merged commit ff38421 into master Apr 16, 2024
3 checks passed
@andrewprzh andrewprzh deleted the fixed_for_3.4 branch May 8, 2024 13:46
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@almiheenko almiheenko Awaiting requested review from almiheenko

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@andrewprzh