Implement sample merging #1026
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Implement sample merging #1026
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1026 +/- ##
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+ Coverage 86.42% 86.73% +0.30%
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Files 28 29 +1
Lines 6109 6233 +124
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+ Hits 5280 5406 +126
+ Misses 829 827 -2 ☔ View full report in Codecov by Sentry. |
Before this change, the file path was required to be provided, but in case the target file did not exist, the script acted as if it was empty. This way optionality was supported, but in a less obvious way. After this change, the file path is allowed to be None, which is treated the same as if it does not exist.
In this update, a new sub-command `merge_samples` has been added to the `micall_docker.py` file. This enables the combination and filtering of FASTQ files from two samples into a single output file. Various arguments have been provided to specify the input files for this new function, allowing for the specification of both the forward and reverse reads of two samples. The command combines the reads from both samples, creating a single FASTQ file. During the process, it also performs censoring.
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Also improve the compression handling.
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Closes #1036