Clean up of the code for parsing manta files / adding structural variants / breakends. Includes both plain refactoring and functional changes.
Changes made:
Functional changes:
14c498c Assumption: the manta files should always add data to an existing dataset, and should therefore never add / change counts for the whole dataset. The code doing this is removed, to avoid unintended changes of the dataset counts.
d1f783b The counter now counts: +1 for every row. This information is only used for logging and the progress bar, due to the commit above. No extra counting of reversed mates is done, since count_entries does not count these.
Bug fix:
be0458c Bug fix: remove not so that the progress bar can be updated.
Code cleanup:
1cf6470 Improve comments etc.
69d9f01 Make the function parse_manta less long by breaking out parts into its own function.
1e698c5, 5521dd6 Break out various code from parse_manta.
TODOs
Look at separation between functions and methods (eg parse_info vs parse_baseinfo).
Describe the pull request:
Pull request long description:
Clean up of the code for parsing manta files / adding structural variants / breakends. Includes both plain refactoring and functional changes.
Changes made:
Functional changes:
14c498c Assumption: the manta files should always add data to an existing dataset, and should therefore never add / change counts for the whole dataset. The code doing this is removed, to avoid unintended changes of the dataset counts.
d1f783b The
counternow counts: +1 for every row. This information is only used for logging and the progress bar, due to the commit above. No extra counting of reversed mates is done, sincecount_entriesdoes not count these.Bug fix:
notso that the progress bar can be updated.Code cleanup:
1cf6470 Improve comments etc.
69d9f01 Make the function
parse_mantaless long by breaking out parts into its own function.1e698c5, 5521dd6 Break out various code from
parse_manta.TODOs
Look at separation between functions and methods (eg
parse_infovsparse_baseinfo).