salzman-lab / SPLASH

MIT License
40 stars 4 forks source link

update parse_anchors string search #8

Closed kaitlinchaung closed 2 years ago

kaitlinchaung commented 2 years ago

In the previous version of parse_anchors, we were searching each read for each anchor, this was quite slow. In this new version, a dictionary is intialized with anchors as keys. The read is then tiled by 1bp and each read tile is checked to see if it belongs to the anchor dict. This results in a faster run time.

github-actions[bot] commented 2 years ago

YAML linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

Once you push these changes the test should pass, and you can hide this comment :+1:

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

github-actions[bot] commented 2 years ago

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

Once you push these changes the test should pass, and you can hide this comment :+1:

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!