CAP3 output in the UGENE Database format

In general, the issue is to change output format of the CAP3 tool in UGENE from ACE to UGENE Database format, so that the data are opened automatically in the Sanger Reads Editor.

Note that this is a basic issue. Other issues in this epic will enhance this feature. In particular, the CAP3 dialog will be modified in terms of UGENE-5991, task report - UGENE-6001, task in the WD - UGENE-6005.

In terms of this issue:

First, fix a bug: quality information is not currently taken into account by CAP3. This happens because the *.qual temporary file has incorrect name. For example, if the FASTA temporary file is called "smth_misc.fa", the *.qual file should be named "smth_misc.fa.qual". There should be no "No file of quality values (.qual) is found" message in the temporary *.info output file.

Second:

• If the ACE file does not contain any contigs, then nothing happens.
• If the ACE file contains one contig:
  • Create the *.ugenedb file.
  • Save the contig sequence like the reference sequence.
  • Save the reads:
    • Take into account a read orientation (do not add "(rev-compl)" to a read name in case of forward orientation).
    • Use input *.ab1 or *.scf files to get the chromatograms.
    • Compare the chromatograms with the reads, trimmed by CAP3 (it is called "clipped" in the CAP3 documentation). Trim the corresponding chromatogram ends. The orientation is also used here.
  • Open the result *.ugenedb file.
• If the ACE file contains more than one contig, repeat the procedure described above for each contig with the corresponding reads. Create the *.ugenedb file with multiple "mc" objects. Open the first object in the Sanger Reads Editor.