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Commits on Nov 27, 2013

• Add a test case based on Daniel Cameron's example of failing FeatureList

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Commits on Oct 16, 2013

• Clean up the majority of compile warnings

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Commits on Apr 27, 2013

• using temporary file instead of updating

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• using temp file for File tmp = File

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Commits on Aug 10, 2012

• fix for unit test failures, use proper temp directory for test output files

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  heuermh

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Commits on Mar 15, 2012

• previous commit, "deleted genome.parsers.fastq and associated test classes (duplicated, they are in their own package, sequencing)" missed removing unit tests

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Commits on Mar 12, 2012

• undid more unnecessary reformatting that made the code harder to read in the Fastq test cases, also removed some unnecessary import statements

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• undid some unnecessary reformatting that made the code harder to read in FastqBuilderTest.java

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• moved fastq classes from biojava3.sequencing.io.fastq to biojava3.genome.parsers.fastq

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  brandstaetter

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Commits on Jan 24, 2011

• Added FeatureHelper which allows you to build indexes based on a feature attribute value. This is then used in GeneFeatureHelper when parsing a gmod gff3 file to quickly find the features that belo…

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  willishf

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Commits on Jan 1, 2011

• Test was failing if the location was at 1 and negative strand because internally stored as 0 and you can't have negative 0

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Commits on Dec 20, 2010

• Minor updates

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  willishf

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Commits on Nov 2, 2010

• Modified in line with latest version of biojava3-core's Sequence interface

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Commits on Oct 22, 2010

• making test less verbose

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Commits on Oct 21, 2010

• Tracking down why testGetProteinSequence fails

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Commits on Oct 20, 2010

• uncommenting broken junit test

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Commits on Oct 18, 2010

• Fixed problem where GmodGFF3 reader was not picking up five_prime_UTR or three_prime_UTR so gene was not the correct start and stop index

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Commits on Oct 15, 2010

• uncommenting broken junit test for now

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• Added support for taking a fasta contig/chromosome file and a fasta gene file where exons are upper case and mapping the genes to chromosome sequences with exon and cds regions. You can then write …

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Commits on Mar 17, 2010

• adding new module biojava3-genome

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