broadinstitute / viral-core / 19176241106

Builds Branch Commit Type Ran Committer Via Coverage
19176241106 ct-swiftseq-demux-integration Consolidate splitcode tests into test_illumina.py - Move all splitcode test classes from test_illumina_splitcode.py to test_illumina.py - Add missing imports (shutil, json, tools.picard) to test_illumina.py - Delete test_illumina_splitcode.py to ... Pull #119 dpark01 github
62.59
19176241878 ct-swiftseq-demux-integration Merge df8d80620 into d3ad25d5f Pull #119 web-flow github
62.61
19175507121 ct-swiftseq-demux-integration Add robust error handling for splitcode summary JSON loading When splitcode summary JSON files are missing or malformed, we now provide comprehensive debugging information to help diagnose the issue faster. Changes to illumina.py (create_splitco... Pull #119 dpark01 github
61.07
19175508368 ct-swiftseq-demux-integration Merge 6465a193a into d3ad25d5f Pull #119 web-flow github
61.07
19175360543 ct-swiftseq-demux-integration Extract splitcode config/keep file generation into testable function - Created generate_splitcode_config_and_keep_files() function to handle config and keep file generation for a single pool - This separates pure text file transformation logic ... push dpark01 github
60.61
19175361248 ct-swiftseq-demux-integration Merge 26cb5b64e into d3ad25d5f Pull #119 web-flow github
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19172223744 ct-swiftseq-demux-integration Add comprehensive module docstring to test_illumina_splitcode.py Added detailed module-level documentation serving as a quick reference for splitcode file formats and behavior: - Explains the purpose of these tests (validating assumptions vs tes... Pull #119 dpark01 github
60.56
19170889014 ct-swiftseq-demux-integration Add comprehensive integration tests for splitcode functionality - Created test_illumina_splitcode.py with 6 test cases validating splitcode behavior - Tests focus on validating our assumptions about splitcode (not testing the external tool itself... Pull #119 dpark01 github
60.17
19166669338 ct-swiftseq-demux-integration Fix rmdup_cdhit_bam to wait for cd-hit-dup completion before reading output Problem: - rmdup_cdhit_bam() was calling cd-hit-dup with background=True, which returns immediately without waiting for the process to finish - FastqToSamTool().execute... Pull #119 dpark01 github
59.82
19157217573 ct-swiftseq-demux-integration Add comprehensive test coverage for create_splitcode_lookup_table and fix bugs This commit adds extensive unit test coverage for the create_splitcode_lookup_table function (formerly create_lut) and fixes several bugs discovered during testing. T... Pull #119 dpark01 github
59.7
19157218116 ct-swiftseq-demux-integration Merge 98d9a675e into d3ad25d5f Pull #119 web-flow github
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19138999502 ct-swiftseq-demux-integration update splitcode Pull #119 dpark01 github
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19139000400 ct-swiftseq-demux-integration Merge 0f60512c5 into d3ad25d5f Pull #119 web-flow github
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18415959536 ct-swiftseq-demux-integration Make plotting and metrics code robust to zero-count data Fix three functions to handle cases where barcodes have zero reads: 1. plot_read_counts(): Check for positive values before setting log scale to avoid matplotlib warnings when all data ... Pull #119 dpark01 github
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18414971484 ct-swiftseq-demux-integration Fix splitcode demux crash when pools have 0 reads Handle the case where splitcode processes 0 reads for a pool, which results in an empty tag_qc array in the summary JSON. Previously this would crash with KeyError: 'tag' when trying to create a D... Pull #119 dpark01 github
58.2