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- 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.

- minor changes to api docs.

- Added support for generating BAM files from fastqs.
- Added a utility that fixes fastqs files that have Uracil bases in them.

ENA-3842

- fixed an issue that ran cram specific processing steps on bam files causing null pointer errors.

Ena 3490

- fixed an overlooked potential issue.
- disabled the unaligned cram file test.

- updated sam2fastq tests.
- added spotless plugin for putting license text in java files.

- updated fastq score generation logic.

- code review followup.
- some changes still incomplete.

- removed more unnecesary code.

- removed commented out/testing/unneeded code.
- added comments.
- updated version number.

- removed tests. created a new utility application instead.
- added todo markers.

- added more tests.

- refactored utility tests.
- added comments.

- created a small test utility class for comparing fastq file data from old and new version.

- added the skipping of non primary alignments and non pf reads.
- refactored code.

- refactored fastq converter to use samreader instead of low level api.
- old code is still present but commented out.