Activity for Ollie Holmes
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Ollie Holmes committed [r2648]
rm ini4j
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get ini4j from mavenCentral
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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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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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minor updates
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if single sample mode, don't attempt to populate normal values
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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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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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removed commented out lines
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refactored method name
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oops
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refactored method and property names
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comment out unused methods
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removed unused methods
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remove normalPileup - replicated in normalOABS
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formatting
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added getOABS method
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remove normal and tumour nucleotides parameters - use OABS instead
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split count by strand
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remove unused attributes
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add test
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util methods for new methods
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remove logging
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beef up test so that I can make some radical changes
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header to contain filter details specific to file type
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add snp id
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reduce logging
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generate bespoke illumina output
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logging
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load snp chip data
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use snpPositions option rather than input array
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null guard rgIds
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don't check that input files exists as it may be s3 file
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updated method name
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another method
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sort snps according to bam header and test
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gets contigs from a bam file and writes them to a file, performing an optional grouping operation
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don't load GATk vcf records that have empty GT fields
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additional test
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use comparator from bam file to order snps, and if bam file contains contigs without "chr", add
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Hi Roland, Thanks for your issue, patch and for finding this bug! I'm doing a little rework in this area and hope to put up a new version soon. Will keep you posted. As for an issue tracker - the sf ticket system is fine. We saw your issue come in and have just been slow in responding to it - apologies. Thanks again, Oliver Holmes
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