malposition of rows with tab and maf format input

[jcd-gh]

The example example_tab.html and example_maf.html showed malposition of rows.
An extra line (i.e. the tittle row) was added to the top of the file, and the corresponding view was shifted by one element.

e.g.:
chr start end ref_allele alt_allele
chr start end ref_allele alt_allele -> view of line 1, should be nothing
chr1 68897222 68897222 G T -> view of line 2, should be line 1
chr1 176760487 176760487 C T -> view of line 3, should be line 2

The problem is shown in version 1.8.0 and the current master branch, version 1.7.0 is not affected.

[Jethro Rainford]

I think this is the same issue as with generic tab delimited files as both are parsed by GenericTable.from_tabfile() which is called here

igv-reports/igv_reports/report.py

Lines 45 to 47 in 0ac3ade

 elif variants_file.endswith(".maf") or variants_file.endswith(".maf.gz") or ( 
         args.sequence is not None and args.begin is not None and args.end is not None): 
     table = GenericTable.from_tabfile(variants_file, args.info_columns, args.sequence, args.begin, args.end, args.zero_based) 

This is addressed in this PR: #89

[Jim Robinson]

@jethror1 is correct. The PR is merged, I will do a 1.8.1 release with this fix later today.

[Jim Robinson]

1.8.1 is released to pypi