This project is mirrored from https://*****:*****@github.com/enasequence/readtools. Pull mirroring updated .
  1. 27 Oct, 2020 1 commit
    • M. Haseeb's avatar
      ENA-4020 · d0209e32
      M. Haseeb authored
      - removed picard from dependency as the version of htsjdk it pulled was causing issues in another project.
      d0209e32
  2. 19 Oct, 2020 1 commit
  3. 16 Oct, 2020 1 commit
    • M. Haseeb's avatar
      ENA-3950 · 375c6982
      M. Haseeb authored
      - allowed U base character in read validation.
      - added the ability convert U bases to T during fastq to BAM conversion.
      375c6982
  4. 15 Oct, 2020 11 commits
  5. 29 Sep, 2020 1 commit
  6. 27 Sep, 2020 1 commit
    • M. Haseeb's avatar
      ENA-3950 · 0281e3be
      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.
      0281e3be
  7. 19 Sep, 2020 3 commits
    • M. Haseeb's avatar
      ENA-3943 · 3549a3df
      M. Haseeb authored
      - fixed a test.
      3549a3df
    • M. Haseeb's avatar
      ENA-3943 · cf1afca6
      M. Haseeb authored
      - updated constructors in Fastq2Sam.
      cf1afca6
    • M. Haseeb's avatar
      ENA-3943 · 162d484c
      M. Haseeb authored
      - added api docs.
      162d484c
  8. 18 Sep, 2020 2 commits
    • M. Haseeb's avatar
      ENA-3943 · 7a1c5e88
      M. Haseeb authored
      - updated version number.
      7a1c5e88
    • M. Haseeb's avatar
      ENA-3943 · 322633cb
      M. Haseeb authored
      - added support for accepting temp directory argument in Fastq2Sam.
      - added a picard argument to skip (ignore) blank lines.
      322633cb
  9. 14 Sep, 2020 1 commit
    • M. Haseeb's avatar
      ENA-3339 · ff41ade1
      M. Haseeb authored
      - added the ability to determine replacement T base case based on the source U base.
      ff41ade1
  10. 08 Sep, 2020 1 commit
    • M. Haseeb's avatar
      ENA-3339 · 275ddb8f
      M. Haseeb authored
      - minor changes to api docs.
      275ddb8f
  11. 03 Sep, 2020 1 commit
    • M. Haseeb's avatar
      ENA-3339 · 2432f175
      M. Haseeb authored
      - Added support for generating BAM files from fastqs.
      - Added a utility that fixes fastqs files that have Uracil bases in them.
      2432f175
  12. 14 Aug, 2020 1 commit
  13. 13 Aug, 2020 2 commits
  14. 11 Aug, 2020 1 commit
  15. 10 Aug, 2020 2 commits
    • M. Haseeb's avatar
      ENA-3490 · 98855a13
      M. Haseeb authored
      - fixed an overlooked potential issue.
      - disabled the unaligned cram file test.
      98855a13
    • M. Haseeb's avatar
      ENA-3490 · 3efacd8a
      M. Haseeb authored
      - updated sam2fastq tests.
      - added spotless plugin for putting license text in java files.
      3efacd8a
  16. 07 Aug, 2020 2 commits
    • M. Haseeb's avatar
      ENA-3490 · ffd09c76
      M. Haseeb authored
      - updated fastq score generation logic.
      ffd09c76
    • M. Haseeb's avatar
      ENA-3490 · 9f981f76
      M. Haseeb authored
      - code review followup.
      - some changes still incomplete.
      9f981f76
  17. 03 Aug, 2020 2 commits
    • M. Haseeb's avatar
      ENA-3490 · 00007d5d
      M. Haseeb authored
      - removed more unnecesary code.
      00007d5d
    • M. Haseeb's avatar
      ENA-3490 · 52e80903
      M. Haseeb authored
      - removed commented out/testing/unneeded code.
      - added comments.
      - updated version number.
      52e80903
  18. 21 Jul, 2020 1 commit
    • M. Haseeb's avatar
      ENA-3490 · 9150e44e
      M. Haseeb authored
      - removed tests. created a new utility application instead.
      - added todo markers.
      9150e44e
  19. 20 Jul, 2020 1 commit
  20. 07 Jul, 2020 2 commits
    • M. Haseeb's avatar
      ENA-3490 · e68ccd9b
      M. Haseeb authored
      - refactored utility tests.
      - added comments.
      e68ccd9b
    • M. Haseeb's avatar
      ENA-3490 · 38d09aa4
      M. Haseeb authored
      - created a small test utility class for comparing fastq file data from old and new version.
      38d09aa4
  21. 23 Jun, 2020 1 commit
    • M. Haseeb's avatar
      ENA-3490 · 3f35bfab
      M. Haseeb authored
      - added the skipping of non primary alignments and non pf reads.
      - refactored code.
      3f35bfab
  22. 22 Jun, 2020 1 commit
    • M. Haseeb's avatar
      ENA-3490 · 12633ea8
      M. Haseeb authored
      - refactored fastq converter to use samreader instead of low level api.
      - old code is still present but commented out.
      12633ea8