Activity for Dan Katzel

  • Dan Katzel Dan Katzel committed [r3365]

    Removed old spec files that have since been mov...

  • Dan Katzel Dan Katzel committed [r3364]

    refactored Rota subtyping to return Map<String,...

  • Dan Katzel Dan Katzel committed [r3363]

    fix for jillion code that can't be committed to...

  • Dan Katzel Dan Katzel committed [r3362]

    bug fix for error path parameter setup

  • Dan Katzel Dan Katzel committed [r3361]

    added missing folder of file system layout spec

  • Dan Katzel Dan Katzel committed [r3360]

    added missing libraries and updated easymock

  • Dan Katzel Dan Katzel committed [r3359]

    added new factory method to take an existing Hi...

  • Dan Katzel Dan Katzel committed [r3358]

    updated executable script to point to new locat...

  • Dan Katzel Dan Katzel committed [r3357]

    restructured main Elvira spec page and pointed ...

  • Dan Katzel Dan Katzel committed [r3356]

    completely reorganized layout of specs for asse...

  • Dan Katzel Dan Katzel committed [r3355]

    fix for changing stain problems from warnings t...

  • Dan Katzel Dan Katzel committed [r3354]

    Added lots more information about how rotavirus...

  • Dan Katzel Dan Katzel committed [r3353]

    Tests for all the code that has changed since t...

  • Dan Katzel Dan Katzel committed [r3352]

    Changes to MergeAndSortBlastXml2Btab

  • Dan Katzel Dan Katzel committed [r3351]

    converted many fasta and fastq programs to use ...

  • Dan Katzel Dan Katzel committed [r3350]

    added more helper methods to get option values ...

  • Dan Katzel Dan Katzel committed [r3349]

    Added example invocations to Usage and UsageBui...

  • Dan Katzel Dan Katzel committed [r3348]

    bugfix for ordering of mixed genotypes. Should...

  • Dan Katzel Dan Katzel committed [r3347]

    VHTNGS-792 StrainCode problems found are now ER...

  • Dan Katzel Dan Katzel committed [r3346]

    Added program to generate sanger lib ids.

  • Dan Katzel Dan Katzel committed [r2457]

    bugfix in percent identity calculation. Accide...

  • Dan Katzel Dan Katzel committed [r3345]

    fixed broken link to file system layout spec

  • Dan Katzel Dan Katzel committed [r3344]

    moved around the spec files to new folder struc...

  • Dan Katzel Dan Katzel committed [r3343]

    Changed the layout of the main Elvira Spec page...

  • Dan Katzel Dan Katzel committed [r3342]

    added Latitude and Longitude validation specs

  • Dan Katzel Dan Katzel committed [r3341]

    added concordion run command to link to run suite

  • Dan Katzel Dan Katzel committed [r3340]

    added latLon Validation to executable

  • Dan Katzel Dan Katzel committed [r3339]

    added LatLon Validation

  • Dan Katzel Dan Katzel committed [r3338]

    Began work on adding Latitude/Longitude validat...

  • Dan Katzel Dan Katzel committed [r3337]

    Created Classes to correctly parse and format L...

  • Dan Katzel Dan Katzel committed [r2456]

    Added support for parsing and writing Non-redun...

  • Dan Katzel Dan Katzel committed [r3336]

    Added ElviraCommandLine.getOptionValueAsRange()

  • Dan Katzel Dan Katzel committed [r3335]

    better handling of values in library id column ...

  • Dan Katzel Dan Katzel committed [r3334]

    better handling of values in library id column ...

  • Dan Katzel Dan Katzel committed [r3333]

    fixed wording slightly

  • Dan Katzel Dan Katzel committed [r3332]

    added H1N1pdm vs seasonal AutoTasker Executable...

  • Dan Katzel Dan Katzel committed [r3331]

    added explicit test to spec to host age only al...

  • Dan Katzel Dan Katzel committed [r3330]

    Rewrote AutoTasker's H1N1pdmVsSeasonal feature ...

  • Dan Katzel Dan Katzel committed [r3328]

    Wrote Java version of Vishal's PdmVsSeasonal De...

  • Dan Katzel Dan Katzel committed [r3327]

    cleaned up a few FindBugs warnings

  • Dan Katzel Dan Katzel committed [r3326]

    Added more pages for the RotaC spec found and f...

  • Dan Katzel Dan Katzel committed [r3325]

    fixed scaffold generation to use ElviraScaffold...

  • Dan Katzel Dan Katzel committed [r3324]

    added more RotaC tests and executable specifica...

  • Dan Katzel Dan Katzel committed [r3323]

    began work on rotaC spec

  • Dan Katzel Dan Katzel committed [r3322]

    added assertions to FindCodonVariants Spec

  • Dan Katzel Dan Katzel committed [r3321]

    added SlowTest JUnit Category and new AllElvira...

  • Dan Katzel Dan Katzel committed [r3320]

    removed guava dependency:

  • Dan Katzel Dan Katzel committed [r3319]

    experimental branch trying out how to modularli...

  • Dan Katzel Dan Katzel committed [r3318]

    fixed broken tests. removed debug lines

  • Dan Katzel Dan Katzel committed [r3317]

    added public method that takes FastaFile

  • Dan Katzel Dan Katzel committed [r3316]

    More work on Jira Sample Tracking Code

  • Dan Katzel Dan Katzel committed [r3315]

    More work on Jira Service API:

  • Dan Katzel Dan Katzel committed [r3314]

    reorganized AutoTasker specs added some scaffol...

  • Dan Katzel Dan Katzel committed [r3313]

    moved SystemExit Stopper code out of test folde...

  • Dan Katzel Dan Katzel committed [r3312]

    added more informative error message for when m...

  • Dan Katzel Dan Katzel committed [r3311]

    more work on new Java Service that interacts wi...

  • Dan Katzel Dan Katzel committed [r3310]

    Made bug fix that caused isFlagAttribute() to a...

  • Dan Katzel Dan Katzel committed [r3309]

    making a branch to make the fix for STS-119 wit...

  • Dan Katzel Dan Katzel committed [r3308]

    Emergency Bug Fix of GLKLib.pm which broke setE...

  • Dan Katzel Dan Katzel committed [r3307]

    minor refactoring of TempDir

  • Dan Katzel Dan Katzel committed [r3306]

    added jira-cli jars that were missing and break...

  • Dan Katzel Dan Katzel committed [r3305]

    initial check in of new JIRA service to replace...

  • Dan Katzel Dan Katzel committed [r3304]

    fixed typo in attribute database name VA-783

  • Dan Katzel Dan Katzel committed [r3303]

    fixed typo in attribute database name VA-783

  • Dan Katzel Dan Katzel committed [r3302]

    fixed typo in attribute database name VA-783

  • Dan Katzel Dan Katzel committed [r3301]

    fixed typo in attribute database name

  • Dan Katzel Dan Katzel committed [r3300]

    release candidate with removed ExtentAttributes...

  • Dan Katzel Dan Katzel committed [r3299]

    minor findbugs fix

  • Dan Katzel Dan Katzel committed [r3298]

    code cleanup and fixes for FindBugs warnings

  • Dan Katzel Dan Katzel committed [r3297]

    updated to latest version of jillion

  • Dan Katzel Dan Katzel committed [r3296]

    Improved BRC metadata date validation and parsing

  • Dan Katzel Dan Katzel committed [r3295]

    modified type so javac inferencing could compil...

  • Dan Katzel Dan Katzel committed [r3294]

    added -flank option to FindStatistically Signif...

  • Dan Katzel Dan Katzel committed [r3293]

    added more helper methods to ElviraCommandLine ...

  • Dan Katzel Dan Katzel committed [r2455]

    added extra step in stream inside equals method...

  • Dan Katzel Dan Katzel committed [r2454]

    added sleep call to help race condition of when...

  • Dan Katzel Dan Katzel committed [r2453]

    changed to use Nucleotide instead of ordinal sh...

  • Dan Katzel Dan Katzel committed [r2452]

    Performance improvements:

  • Dan Katzel Dan Katzel committed [r2451]

    Bug Fix for sequence.iterator(Range) for refere...

  • Dan Katzel Dan Katzel committed [r2450]

    improved method signatures on VariableWidthSlic...

  • Dan Katzel Dan Katzel committed [r3292]

    cleaning up Sample object model.

  • Dan Katzel Dan Katzel committed [r3291]

    added more autoTasker executable spec pages

  • Dan Katzel Dan Katzel committed [r3290]

    code cleanup and refactoring

  • Dan Katzel Dan Katzel committed [r3289]

    bug fix to close open temp workbooks

  • Dan Katzel Dan Katzel committed [r3288]

  • Dan Katzel Dan Katzel committed [r3287]

    updated to latest jillion with better error rep...

  • Dan Katzel Dan Katzel committed [r2449]

    Changed IOUtil.delete() methods to use Java 7 N...

  • Dan Katzel Dan Katzel committed [r3286]

    added cell style to center numbers like the ser...

  • Dan Katzel Dan Katzel committed [r3285]

    working version of grid multirun createClosureA...

  • Dan Katzel Dan Katzel committed [r3284]

    working version of grid multirun createClosureA...

  • Dan Katzel Dan Katzel committed [r3283]

    fixed null root output dir bug and bug that ski...

  • Dan Katzel Dan Katzel committed [r3282]

    fixed null root output dir bug and bug that ski...

  • Dan Katzel Dan Katzel committed [r3281]

    changed working dir during grid submissions

  • Dan Katzel Dan Katzel committed [r3280]

    changed working dir during grid submissions

  • Dan Katzel Dan Katzel committed [r3279]

    removed line to not delete more intermediate t...

  • Dan Katzel Dan Katzel committed [r3278]

    removed line to delete intermediate temp files ...

  • Dan Katzel Dan Katzel committed [r3277]

    removed line to delete intermediate temp files ...

  • Dan Katzel Dan Katzel committed [r3275]

    fixed typo in config file for path to single cr...

  • Dan Katzel Dan Katzel committed [r3274]

    fixed typo

  • Dan Katzel Dan Katzel committed [r3273]

    fixed typo

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