Initial import.

git-svn-id: http://www.molgenis.org/svn/standalone_tools@8138 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added standalone runnable JARs that perform data conversion. Manual and example included.

git-svn-id: http://www.molgenis.org/svn/standalone_tools@8139 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Initial import.

git-svn-id: http://www.molgenis.org/svn/standalone_tools@9029 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Upload of new version of this project. TODO: make standalone source for BinToCsv and CsvToBin which compiles to a regular (small) JAR

git-svn-id: http://www.molgenis.org/svn/standalone_tools@9031 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Tried to optimize TriToBin though it doesnt seem to matter much, bottleneck is probably not the writing but the reading.

git-svn-id: http://www.molgenis.org/svn/standalone_tools@9032 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Created standalone implementations of the CsvToBin and BinToCsv tools. The resulting runnable JARs are not 45 MB but 65 kB :)

git-svn-id: http://www.molgenis.org/svn/standalone_tools@9933 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added a standalone tool: TriToBinSlice. Convert from TriTyper to xQTL binary format while making a subselection of individuals. The selection is passed by a file, similar to Individuals.txt in the TriTyper folder you want to convert, but with fewer individuals in it.

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10045 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Working on TriTyper to Plink (TPED/TFAM) convertor.

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10091 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Created 'TriToPlinkSlice' tool. Convert from TriTyper to Plink TPED+TFAM format while making a subselection of individuals and appending phenotypes to the FAM file.

Syntax example:
java -jar TriToPlinkSlice.jar BrainsetTriTyper/ output subsetPlusPheno.txt

Get help:
java -jar TriToPlinkSlice.jar

Example individuals + pheno file at:
examples/TriToPlinkSlice-exampleSubsetPlusPheno.txt

Standalone JAR at:
jars/TriToPlinkSlice.jar

Source code at:
src/tritoplinkslice

Manual at:
manuals/TriToPlinkSlice.txt

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10106 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Working on a new standalone tool: CsvToBinOnDir. This tool converts a directory with CSV matrix files to xQTL binary matrices. The conversion arguments are passed via a MOLGENIS/XGAP format file with 'Data' entities. At the end you will receive a report with the verification/conversion results for each matrix. Todo: test a bit, polish, add JAR, manuals, etc. Also fixed a mixup in the inline help for TriToPlinkSlice.

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10195 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added manual, JAR and example for CsvToBinOnDir tool.

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10208 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added special LifeLines flavour of the TriToPlinkSlice tool. This version creates pseudonymized output based on an additional column in the slice file. You can also limit the output to only create a TFAM or TPED file, or do both at once as usual.

Runnable JAR: jars/TriToPlinkLifeLines.jar
Please read the manual for details: manuals/TriToPlinkLifeLines.txt

Example of a slice file with pseudonyms: examples/TriToPlinkLifeLines-exampleSubsetPseudo.txt
Inline help from the tool: java -jar TriToPlinkSlice.jar

Example usage:
java -jar TriToPlinkLifeLines.jar F BrainsetTriTyper/ myresults subsetpseudo.txt
java -jar -Xmx1g TriToPlinkLifeLines.jar B LifeLinesTriTyper/ study9 pseudo_for_userX.txt

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10262 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Committed TODOs for Thursday

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10572 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Different way of handling unmatched individuals

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10605 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Fixed bug, removing unnecessary code

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10606 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Made writing whole tuples to std out optional

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10610 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Give user some more feedback on progress

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10611 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added the 'user.war' service to the standalone tools. Details in the manual.

git-svn-id: http://www.molgenis.org/svn/standalone_tools@10785 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added new standalone tool: PlinkbinToCsv

Convert from binary Plink format (BED+BIM+FAM) format to Molgenis readable CSV format (individuals + SNPs + genotype matrix). Input files are expected to have the same name (e.g. 'mydata'), with the different extensions (.bim, .bed and .fam) and must all exist. Output files are also based on this name ('mydata') with different suffixes (X_individuals.txt, X_snps.txt, X_genotypes.txt) and may not yet exist when the tool is started.

Example usage:
java -jar -Xmx1g PlinkbinToCsv.jar mydata

Get help:
java -jar PlinkbinToCsv.jar

git-svn-id: http://www.molgenis.org/svn/standalone_tools@11051 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Worked on PLINK to CSV, almost working, except for problem with stop/start byte sometimes...

git-svn-id: http://www.molgenis.org/svn/standalone_tools@11120 42de9c89-b41c-0410-9fa9-f33e7b6bda7a