broadinstitute / viral-ngs
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master: 23%

LAST BUILD BRANCH: ct-krakenuniq-summary-kmer-filter
DEFAULT BRANCH: master
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LAST BUILD ON BRANCH ct-add-mafft
branch: ct-add-mafft
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Relevant lines Covered
4061 RELEVANT LINES 2473 COVERED LINES
1.22 HITS PER LINE
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Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
895 ct-add-mafft added .coveragerc so code can be excluded from test coverage reports blocks can either be commented with “#pragma: no cover”, or raise NotImplementedError. __repr__ methods are also ignored, as is ‘if __name__ == “__main__” ‘ push tomkinsc travis-ci pending completion  
869 ct-add-mafft manual closure of input files in transposeChromosomeFiles() input files are now closed in transposeChromosomeFiles(), before the CPython GC would do so upon returning to the calling function, multichr_mafft(). confirmed via lsof push tomkinsc travis-ci pending completion  
866 ct-add-mafft changes in response to feedback in pull request #122 in MAFFT tool, there is now a check for uniqueness of sequence IDs, both within each input file (if multiple are specified), and within the combined input file fed to mafft.bat. outDirectory i... push tomkinsc travis-ci pending completion  
863 ct-add-mafft Added multichr_mafft Added argparse function multichr_mafft to perform alignment on multiple chromosomes stored in sample-specific FASTA files. Added a helper function used as a pre-processing step to MAFFT that transposes chromosome info from se... push tomkinsc travis-ci pending completion  
860 ct-add-mafft added type requirements to mafft arguments int and float types are specified for MAFFT argparse arguments to obviate the need for later typecasting push tomkinsc travis-ci pending completion  
858 ct-add-mafft fixes in response to feedback —local pair and —global pair are now mutually exclusive via argparse add_mutually_exclusive_group(). The —maxiter argument note now mentions that the default changes to 1000 if —localpair or —globalpair is specified... push tomkinsc travis-ci pending completion  
856 ct-add-mafft removed debug statements removed debug statements push tomkinsc travis-ci pending completion  
855 ct-add-mafft fix to mafft verify command, call command The mafft binary is called by a shell script that comes with the mafft package. This shell script relies on $pwd being the mafft package directory. Differences in environment can change the subprocess pw... push tomkinsc travis-ci pending completion  
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