Opening of VCF file with invalid lines

Variants in a VCF file are stored in lines, i.e. each variant is described in one line. Therefore, if a line is invalid, it can be skipped and the file can be parsed further.

In the current UGENE version, when a VCF file contains an invalid line, the file is not opened and an error notification is shown.

The following should be done instead:

• The valid records must be visualized in the GUI
• A warning notification must appear. When the notification is clicked, a report is opened. The report contains detailed information about each invalid record: the line number and the problem occurred.

Sample VCF files are attached:

• G55421.annotated.vcf - the file can't be opened in UGENE, but can be in IGV.
• G55414.annotated.vcf, G55430.annotated.vcf - the files can't be opened in neither in UGENE, nor in IGV.
• G55431.annotated.vcf - can be opened without errors.