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igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
MIT License
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malposition of rows with tab and maf format input #88

Closed jcd-gh closed 1 year ago

jcd-gh commented 1 year ago

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.

jethror1 commented 1 year ago

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

https://github.com/igvteam/igv-reports/blob/0ac3ade3996dc427162d2c48463811f8816756e2/igv_reports/report.py#L45-L47

This is addressed in this PR: https://github.com/igvteam/igv-reports/pull/89

jrobinso commented 1 year ago

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

jrobinso commented 1 year ago

1.8.1 is released to pypi