GitLab

ENA-3431

- added and modified unit tests for Bam and Fastq scanner run durations.

- added timeboxed valdiation support for SAM and Fastq formats.

- added a small utility to check if bam files have reverse reads in them.
- updated year text in the license text.

# 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

ENA-4123

- 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.

ENA-3407

- removed calculation of pair stats on single fastq validation.

ENA-4072

- removed read count logging from Fastq and BAM/CRAM validation.
- refactored/improved CRAM validation code.

ENA-3934

- review followup.

- added the ability to find and return total read and base count in Fastq2Sam.

- removed picard from dependency as the version of htsjdk it pulled was causing issues in another project.

ENA-3950

- allowed U base character in read validation.
- added the ability convert U bases to T during fastq to BAM conversion.

- fixed some problems that new changes caused in other projects.
- added a new test to look for such problems in future.

- recovered SamplingDataConsumer becuase its being in use in another project.

- major refactor of FastqSpot class and all the relevant code.

- refactored data spot reader to improve its readibility and reduce chances of bugs.

- major refactor of normalization and spot data reading code.

- fixed a small overlooked problem.

- PR followup.

- PR followup.

- 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.

ENA-3950

- Updated DataSpot class to throw a proper invalid base character exception so calling code can easily handle it.
- Some improvements to previously added code.

- fixed a test.

- updated constructors in Fastq2Sam.

- added api docs.

- updated version number.

- added support for accepting temp directory argument in Fastq2Sam.
- added a picard argument to skip (ignore) blank lines.

- added the ability to determine replacement T base case based on the source U base.