AdamaJava Activity
Status: Alpha
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grendeloz
Activity for AdamaJava
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Vincent Gassend posted a comment on discussion General Discussion
Hi, I use qAmplicon to design amplicons for variant verification. I have been using this software for a long time, and it works as expected. But I tried to use the "dbsnp" option, and nothing happens... It seems that the option is not taken into account. This software is a few years old, and I can't find anything about it. Do you have any feedback on this particular problem? Thank you for your help, Vincent
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christina Xu committed [r2654]
move plugin application to subprojects
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apply plugin: 'application' from mainClassName
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add subporject/build/lib to root adama lib
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copy jar files to adama at subproject stage
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use file.absolutePath to get root adama/build/lib
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move repeated task from sub project to root
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Ollie Holmes committed [r2648]
rm ini4j
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get ini4j from mavenCentral
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tidy up all sub build file
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fixing build: qsv testcompile
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fixing build
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fix build problem
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delete debug code
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solve build dependecy locateion
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mistake hdf-java on dependency
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update build on qbasepileup
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update build in qpileup
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add unzipped dependency for qbasepileup
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add unzip for dependency folder in build of qpileup
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update build file, download dependency from maven
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remove debug code, add unit test
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add an temporary mode Vcf2mafTmp which can convert old style vcf to maf with overlap pileup counts
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change optional maf column ACSNP to ACLAP
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add base quality check for snps on overlap mode
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genomeinfo-sf committed [r2630]
Labeled automatically by TeamCity
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tidy-up
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use junit to handle file creation and deletion
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use junit to handle file creation and deletion
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fixing errors
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tidy-up
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don't write to file
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new test
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fixing errors
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use Map.forEach
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fixing errors
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modularise code
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remove unused code
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private final
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remove unnecessary sc
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clean unit test output
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removed unnecessary casts
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removed unnecessary casts
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update stream usage
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dont stream
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make final
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make final
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removed unused vars, make final
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make final and private
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make static vars final, use from options
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make vars static and final and private
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removed unused methods
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trim some fat
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minor change
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cast to appropriate type
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use ChrPosition rather than ChrRangePosition to query map
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add ACLAP for overlap pileup on qannotate
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merged from branch manually, snpPileupMode is replaced by overlapMode
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minor updates
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if single sample mode, don't attempt to populate normal values
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revise build
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updated method name
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minor updates
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minor updates
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more efficient algorithms
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minor updates
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minor updates
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refactored to perform a little quicker
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make method static, add test
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add mergeVcfRec
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remove qmaths
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merged from long-lived qsnp branch
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merging
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merged from trunk
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merging
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merging
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merging
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snp chip work
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removed commented out code
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updates
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additional test
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support snp chip files
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merged from trunk
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merge from trunk
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more appropriate name
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test for new class
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Labeled automatically by TeamCity
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renameing tag
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removing more unwanted tags
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removed commented out code
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removed unwanted tags
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removed build-20 tag
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removed build-1 tag
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removed commented out lines again
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Labeled automatically by TeamCity
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removed commented out lines
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Labeled automatically by TeamCity
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Labeled automatically by TeamCity
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Labeled automatically by TeamCity
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Labeled automatically by TeamCity
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