Remove N padding for out-of-range bases in read-sequence. #121
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov Report
@@ Coverage Diff @@
## master #121 +/- ##
==========================================
- Coverage 84.93% 84.91% -0.03%
==========================================
Files 62 62
Lines 4202 4196 -6
Branches 412 412
==========================================
- Hits 3569 3563 -6
Misses 221 221
Partials 412 412
Continue to review full report at Codecov.
|
alumi
force-pushed
the
fix/sequence-out-of-range
branch
from
e54ed1c to
39efba3
Compare
totakke
reviewed
Nov 13, 2017
src/cljam/io/fasta/reader.clj
Outdated
| (when-let [len (:len (fasta-index/get-header fai name))] | ||
| (let [start' (max 1 (or start 1)) | ||
| end' (min len (or end len))] | ||
| (when (<= 1 start' end' len) |
There was a problem hiding this comment.
(<= 1 start') is obvious from (max 1 (or start 1), and (<= end' len) is obvious from (min len (or end len)). So this predicate can be simplified as (<= start' end').
src/cljam/io/twobit/reader.clj
Outdated
| (.toString cb))))) | ||
| start' (max 1 (or start 1)) | ||
| end' (min len (or end len))] | ||
| (when (<= 1 start' end' len) |
There was a problem hiding this comment.
Same as the comments in fasta.reader.
|
Thank you for the comment! |
totakke
approved these changes
Nov 13, 2017
|
Thanks! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Summary
Fix for #120 comment
Tests
lein test :all🆗