Wrapped priority Picard tools (#122) and added program record to Filter PIP-seq output (#144) #187
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Matched this branch with changes made to the dev branch when Erik-Branch was merged. This will allow a simple merge in the future as this branch is basically a fork of dev now. Added new Picard tool DownsampleSam. The tool is in the DownsampleSamFile class and its supporting window class is called DownsampleSamFileWindow Added scroll functionality to the BAM Manipulation window in allow the user to select DownsampleSam
#122 Added two classes. ValidateSamWrapper and ValidateSamWindow. The ValidateSam tool allows for customization of the validation mode, maximum output in verbose mode, whether to generate an index or not, and output destination. Currently outputs a html file. Minor bug fixing related to DownsampleSam. The program now works as intended. Reworded the javadocs. Still unsure if those javadocs are perfect.
#122 Removed the dashes from the JavaDocs in the Wrapper classes for ValidateSam and DownsampleSam. Added a short JavaDocs that references the Wrapper in the Window classes. Also, reworked the Max Output feature in ValidateSam a slight bit so it has 100 (default) in the text box to show the user what that default value is.
#122 Added two new tools. SamFormatConverter converts a SAM file to a BAM file or vice versa. SamtoFastq converts a BAM file to a FASTQ file. It has two features both of which are experiencing errors causing no output. However the default configuration runs fine. Did some minor code cleanup on ValidateSam as well. Along with an additial condition being handled in DownsampleSam. Before, when a user entered a desired maximum number of reads to be outputted that is larger than the total number of reads, the program would default to 0.5 probability without alerting the user. A JOptionPane now tells the user this fact. Also, added the option to load a SAM file instead of a BAM file for DownsampleSam and ValidateSam.
Added NormalizeFasta and CollectBaseDistributionByCycle Picard tools and added the wrapper for the FilterSamReads tool. Refactored BAIIndexer to BAIIndexerWrapper and Window to match with other tools. The charting feature for CollectBaseDistributionByCycle experiences an unknown error on my end. I am unsure if this has something to do with my R install or the code itself.
#122 Created a Wrapper and Window class for the Picard tool called FilterSamReads.
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Erik, thanks for making my job easy 👍