Refactor to_numeric_ignore_errors to to_numeric_ignore_columns
This change is slightly cleaner because it addresses the root issue that some columns are strings (and can therefore not be converted to numeric types). Now if an error does occur when converting the dfs to numeric types it won't be swallowed up.
Add documentation to to_numeric_ignore_columns
Extract out quantification window coordinate function
Refactor get_quant_window_coordinates function into two
The rationale behind this is that the behavior around the cloned amplicon is quite different than if the qwc are specified directly for the amplicon.
Handling qwc: add unit tests, refactor some more and add documentation
Extract out get_relative_coordinates function
This function just computes the relative indexes without doing an alignment.
Add clarifying unit tests for get_relative_coordinates
Refactor cloned indexes to use ref_positions instead of s1inds
fixed function for getting cloned qwc idxs
added tests for cloned qwc function
Introduce pandas sorting in CRISPRessoCompare (#47)
Fix interleaved fastq input in CRISPRessoPooled and suppress CRISPRessoWGS params (#42)
Extract out split_interleaved_fastq function to CRISPRessoShared
Implement splitting interleaved fastq files in CRISPRessoPooled
Suppress split_interleaved_input from CRISPRessoWGS parameters
Suppress other parameters in CRISPRessoWGS
Move where interleaved fastq files are split to be trimmed properly
Bug Fix - 367 (#35)
Fixed references to ref_names_for_pe
removed extra tabs
trying to match empty line, no tabs
changed references to ref_names[0]
Mckay/pd warnings (#45)
refactor errors='ignore' to try except
refactored integer slice to iloc[]
moved to_numeric try except to function
Refactor to_numeric_ignore_errors to to_numeric_ignore_columns
This change is slightly cleaner because it addresses the root issue that some columns are strings (and can therefore not be converted to numeric types). Now if an error does occur when converting the dfs to numeric types it won't be swallowed up.
Add documentation to to_numeric_ignore_columns
removed if check
implemented last test
changed NT to BadParameterException
changed tests, NT to BadParameter exceptions
Uncomment and correct tests for get_relative_coordinates
finished qwc tests
0 is an acceptable qwc
new get_relative_coords function
added relative coordinate tests
removed unused functions
formatting
check for 0 qwc
remove test code
remove comment
Move read filtering to after merging in CRISPResso (#39)
Move read filtering to after merging
This is in an effort to be consistent with the behavior and results of CRISPRessoPooled.
Properly assign the correct file names for read filtering
Mckay/pd warnings (#45)
refactor errors='ignore' to try except
refactored integer slice to iloc[]
moved to_numeric try except to function
Refactor to_numeric_ignore_errors to to_numeric_ignore_columns
This change is slightly cleaner because it addresses the root issue that some columns are strings (and can therefore not be converted to numeric types). Now if an error does occur when converting the dfs to numeric types it won't be swallowed up.
Extract out quantification window coordinate function
Refactor get_quant_window_coordinates function into two
The rationale behind this is that the behavior around the cloned amplicon is quite different than if the qwc are specified directly for the amplicon.
Handling qwc: add unit tests, refactor some more and add documentation
Extract out get_relative_coordinates function
This function just computes the relative indexes without doing an alignment.
Add clarifying unit tests for
get_relative_coordinatesRefactor cloned indexes to use ref_positions instead of s1inds
fixed function for getting cloned qwc idxs
added tests for cloned qwc function
Introduce pandas sorting in CRISPRessoCompare (#47)
Fix interleaved fastq input in CRISPRessoPooled and suppress CRISPRessoWGS params (#42)
Extract out split_interleaved_fastq function to CRISPRessoShared
Implement splitting interleaved fastq files in CRISPRessoPooled
Suppress split_interleaved_input from CRISPRessoWGS parameters
Suppress other parameters in CRISPRessoWGS
Move where interleaved fastq files are split to be trimmed properly
Bug Fix - 367 (#35)
removed extra tabs
trying to match empty line, no tabs
Mckay/pd warnings (#45)
refactor errors='ignore' to try except
refactored integer slice to iloc[]
moved to_numeric try except to function
Refactor to_numeric_ignore_errors to to_numeric_ignore_columns
This change is slightly cleaner because it addresses the root issue that some columns are strings (and can therefore not be converted to numeric types). Now if an error does occur when converting the dfs to numeric types it won't be swallowed up.
removed if check
implemented last test
changed NT to BadParameterException
changed tests, NT to BadParameter exceptions
Uncomment and correct tests for
get_relative_coordinatesfinished qwc tests
0 is an acceptable qwc
new get_relative_coords function
added relative coordinate tests
removed unused functions
formatting
check for 0 qwc
remove test code
remove comment
Move read filtering to after merging in CRISPResso (#39)
Move read filtering to after merging
This is in an effort to be consistent with the behavior and results of CRISPRessoPooled.
Properly assign the correct file names for read filtering
Add space around operators
GitHub actions on pr (#51)
Run integration tests on pull_request
Run pytest on pull_request
Run pylint on pull_request
Run tests on PR only when opening PR (#53)
Update reports (#52)
Update report changes
Switch branch of integration test repo
Remove extraneous
crispresso_data_pathPoint integration tests back to master