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Wrap priority Picard tools into GUI #122

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owlang opened this issue Jun 6, 2023 · 0 comments · May be fixed by #187
Open

Wrap priority Picard tools into GUI #122

owlang opened this issue Jun 6, 2023 · 0 comments · May be fixed by #187
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owlang commented Jun 6, 2023 •
edited by benjaminbeer256
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Build a Window and GUI wrapper for the following tools and organize them into the following tool groups:

Name Implemented @pg ScriptManager @pg Latest Picard
BAM Manipulation
BAMMarkDuplicates Y Y Y
DownsampleSam Y N Y
AddCommentsToBAM Y N N
FilterSamReads Y N N
NormalizeFasta Y N/A N/A
ValidateSamFile Y N/A N/A
BAM Statistics
CollectBaseDistributionByCycle Y N/A N/A
BAM Format Converter
SamToFastq Y N/A N/A
SamFormatConverter (BAM to SAM and SAM to BAM) Y N N
@owlang owlang assigned owlang and Erikpav and unassigned owlang Jun 6, 2023
Erikpav added a commit that referenced this issue Jun 8, 2023
@Erikpav
Added new features to DownsampleSamWrapper
531570a 
#122 Added a custom seed selection and an option to selection a desired number of reads. However, the read # selection has an issue where it is not the exact number of reads the user wants. It can be slightly too many or too little.

Also, renamed the new tools to match a theme of Wrapper and Window.

Reworded the tool description for DownsampleSam.
Erikpav added a commit that referenced this issue Jun 9, 2023
@Erikpav
Added ValidateSam Picard tool
cf1961e 
#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.
Erikpav added a commit that referenced this issue Jun 9, 2023
@Erikpav
Updated JavaDocs for Validate and Downsample
3480a2d 
#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.
Erikpav added a commit that referenced this issue Jun 12, 2023
@Erikpav
Added SamFormatConverter and SamtoFastq
78754ec 
#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.
Erikpav added a commit that referenced this issue Jul 18, 2023
@Erikpav
Added FilterSamReads
c223950 
#122 Created a Wrapper and Window class for the Picard tool called FilterSamReads.
@owlang owlang assigned benjaminbeer256 and unassigned Erikpav Nov 19, 2024
@benjaminbeer256 benjaminbeer256 linked a pull request Dec 3, 2024 that will close this issue
Wrapped priority Picard tools (#122) and added program record to Filter PIP-seq output (#144) #187
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