This project is mirrored from https://*****:*****@github.com/enasequence/readtools.
Pull mirroring updated .
- 25 Jan, 2021 2 commits
- 23 Jan, 2021 1 commit
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M. Haseeb authored
- added timeboxed valdiation support for SAM and Fastq formats.
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- 15 Jan, 2021 1 commit
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M. Haseeb authored
- added a small utility to check if bam files have reverse reads in them. - updated year text in the license text.
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- 14 Jan, 2021 5 commits
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Yevhen Ivanov authored
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Yevhen Ivanov authored
# Conflicts: # build.gradle # src/main/java/uk/ac/ebi/ena/readtools/sam/Sam2Fastq.java # src/test/java/uk/ac/ebi/ena/readtools/sam/Sam2FastqTest.java
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M. Haseeb authored
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Rasko Leinonen authored
ENA-4123
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M. Haseeb authored
- set the default value of the reverse flag on sam to fastq converter to true. - added a unit test to verify it works as expected.
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- 17 Dec, 2020 1 commit
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Yevhen Ivanov authored
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- 09 Dec, 2020 2 commits
- 04 Dec, 2020 2 commits
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Rasko Leinonen authored
ENA-4072
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M. Haseeb authored
- removed read count logging from Fastq and BAM/CRAM validation. - refactored/improved CRAM validation code.
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- 02 Dec, 2020 2 commits
- 30 Nov, 2020 1 commit
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M. Haseeb authored
- review followup.
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- 30 Oct, 2020 1 commit
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M. Haseeb authored
- added the ability to find and return total read and base count in Fastq2Sam.
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- 27 Oct, 2020 1 commit
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M. Haseeb authored
- removed picard from dependency as the version of htsjdk it pulled was causing issues in another project.
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- 19 Oct, 2020 1 commit
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M. Haseeb authored
ENA-3950
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- 16 Oct, 2020 1 commit
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M. Haseeb authored
- allowed U base character in read validation. - added the ability convert U bases to T during fastq to BAM conversion.
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- 15 Oct, 2020 11 commits
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M. Haseeb authored
- fixed some problems that new changes caused in other projects. - added a new test to look for such problems in future.
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M. Haseeb authored
- recovered SamplingDataConsumer becuase its being in use in another project.
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Rasko Leinonen authored
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M. Haseeb authored
- major refactor of FastqSpot class and all the relevant code.
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M. Haseeb authored
- refactored data spot reader to improve its readibility and reduce chances of bugs.
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M. Haseeb authored
- major refactor of normalization and spot data reading code.
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Rasko Leinonen authored
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M. Haseeb authored
- fixed a small overlooked problem.
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M. Haseeb authored
- PR followup.
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M. Haseeb authored
- PR followup.
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M. Haseeb authored
- moved fastq to sam implementation from Frankenstein to this repository and renames it to EnaFastq2Sam. - changed feeder/eater terminologies and replaced them with producer/consumer.
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- 29 Sep, 2020 1 commit
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M. Haseeb authored
ENA-3950
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- 27 Sep, 2020 1 commit
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M. Haseeb authored
- Updated DataSpot class to throw a proper invalid base character exception so calling code can easily handle it. - Some improvements to previously added code.
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- 19 Sep, 2020 3 commits
- 18 Sep, 2020 2 commits
- 14 Sep, 2020 1 commit
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M. Haseeb authored
- added the ability to determine replacement T base case based on the source U base.
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