Last bug fixes and additions for v0.13 CLI release#50
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WilliamKMLai merged 6 commits intomasterfrom Jan 6, 2021
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bug: max/min insert filter option validation did not account for default negative values add validation: midpoint option to automatically flip option "require PE" which will better mimic GUI version of the tool
Pattern (regex object) check to allow for more than one character strings for the filter string input option (only single ATCG allowed before this commit) Fix some indentation formatting and explicitly initialize PrintStream object as null in the script class for the FilterPIPseq tool. This part should not change the behavior.
The GFFtoBED extension check in the CLI class was looking for the wrong extension. This bug is fixed with this commit.
Change default plot output to not include a title. Before this commit default was to add filename as default title for the composite plot.
AggregateDataCLI was missing a basic option check for negative index values for the starting row or column. This commit adds this basic validation. More validation may be added in the future.
Using the Pattern and Match regular expression objects, check that the motif string is composed of capital ATCG characters. Be sure to update this validation if IUPAC degenerate nucleotide symbols are supported in the future.
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This pull request includes additions and fixes to various validations of the user input for the CLI tools.
BAM_Format_Converter/BAMtobedGraphCLI
BAM_Format_Converter/BAMtoBEDCLI
BAM_Format_Converter/BAMtoGFFCLI
BAM_Format_Converter/BAMtoscIDXCLI
BAM_Manipulation/FilterforPIPseqCLI
Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI
Figure_Generation/CompositePlotCLI
Read_Analysis/AggregateDataCLI
Sequence_Analysis/SearchMotifCLI