ENA-4969
- Simplified fastq scanner for better readibility. - Refactored code. Added more comments and TODOs for important things to change in future. - Updated tests.
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- src/main/java/uk/ac/ebi/ena/readtools/loader/common/FileCompression.java 6 additions, 4 deletions...k/ac/ebi/ena/readtools/loader/common/FileCompression.java
- src/main/java/uk/ac/ebi/ena/readtools/loader/common/converter/AbstractReadConverter.java 2 additions, 2 deletions...dtools/loader/common/converter/AbstractReadConverter.java
- src/main/java/uk/ac/ebi/ena/readtools/loader/common/converter/AutoNormalizeQualityReadConverter.java 10 additions, 9 deletions...r/common/converter/AutoNormalizeQualityReadConverter.java
- src/main/java/uk/ac/ebi/ena/readtools/loader/common/converter/ReadConverter.java 9 additions, 9 deletions.../ena/readtools/loader/common/converter/ReadConverter.java
- src/main/java/uk/ac/ebi/ena/readtools/loader/common/converter/ReadReader.java 11 additions, 11 deletions...ebi/ena/readtools/loader/common/converter/ReadReader.java
- src/main/java/uk/ac/ebi/ena/readtools/loader/fastq/FastqIterativeWriterIterator.java 9 additions, 4 deletions.../readtools/loader/fastq/FastqIterativeWriterIterator.java
- src/main/java/uk/ac/ebi/ena/readtools/loader/fastq/PairedFastqWriter.java 1 addition, 1 deletion.../ac/ebi/ena/readtools/loader/fastq/PairedFastqWriter.java
- src/main/java/uk/ac/ebi/ena/readtools/loader/fastq/Read.java 1 addition, 1 deletionsrc/main/java/uk/ac/ebi/ena/readtools/loader/fastq/Read.java
- src/main/java/uk/ac/ebi/ena/readtools/validator/ReadsValidator.java 3 additions, 8 deletions...ava/uk/ac/ebi/ena/readtools/validator/ReadsValidator.java
- src/main/java/uk/ac/ebi/ena/readtools/webin/cli/rawreads/BloomWrapper.java 6 additions, 5 deletions...ac/ebi/ena/readtools/webin/cli/rawreads/BloomWrapper.java
- src/main/java/uk/ac/ebi/ena/readtools/webin/cli/rawreads/FastqScanner.java 135 additions, 101 deletions...ac/ebi/ena/readtools/webin/cli/rawreads/FastqScanner.java
- src/test/java/uk/ac/ebi/ena/readtools/common/producer/AutoNormalizerReadProducerTest.java 3 additions, 3 deletions...tools/common/producer/AutoNormalizerReadProducerTest.java
- src/test/java/uk/ac/ebi/ena/readtools/webin/cli/rawreads/FastqScannerTest.java 42 additions, 0 deletions...bi/ena/readtools/webin/cli/rawreads/FastqScannerTest.java
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