Fix v2.1.2 #383
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Fix v2.1.2 #383
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Also modified the calculation of the junction location to match what is currently expected from the portcullis file
…s impossible without digging really deeply into how Python deals with pipes and streams, so we will shelve it for now.
…without providing a file format.
… 'pacbio.bam' in the sample_data, fixing the system tests
Codecov Report
@@ Coverage Diff @@
## master #383 +/- ##
==========================================
+ Coverage 81.58% 85.54% +3.95%
==========================================
Files 106 110 +4
Lines 19314 19318 +4
==========================================
+ Hits 15757 16525 +768
+ Misses 3557 2793 -764 |
…ocus classes. Minor bugfixes after introducing the changes.
…ing in multiprocessing.
…rsing of input list files.
…pare with BAM files.
…programs utilities to create logs
…culated once and retrieved lazily using a LRU cache
… of the code that seem unreachable or anyway never reached.
… Added a batch of tests to make sure that section of the code is properly covered.
…defined in the database
…ered by transcripts persistently having a score below 0. Properly tested now. Also expanded the unit-test suite.
…mble/mikado pipeline in coverage analysis. Added tests for the 'is_intersecting' and 'define_graph' sections of superlocus.
…so, added a test for the junction loading.
…s) for BED12 and ORF loading. CHANGELOG updated.
This was
linked to
issues
Mar 13, 2021
…Mikado util stats to deal with BAM files.
…irectory needed to get set before we executed the functions to create the loggers.
…oading. Now Mikado serialise will immediately stop and exit if there is a mismatch between the TSV queries and/or targets, on one hand, and the query/target FASTA databases, on the other. Refactored the Hit and Hsp classes so that it is easier to create instances, for unit-testing. The old __init__ have now become class methods to create instances from Hit/Hsps objects coming from the BLAST XML parsers.
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Fix #381
Fix #382