v.0.7.3

New

New option --gene-arrows now lets you display annotations from a gff direction dependent as arrows.

Example without arrows:

Example with arrows:

What's Changed

• Enable arrows in the gene vis by @jonas-fuchs in #20
• Full Changelog: v.0.7.2...v.0.7.3

v.0.7.2

virHEAT v.0.7.2

Enhancements:
Can now parse vcf files with multiple variants reported in one vcf line. Thereby, giving support for FreeBayes vcf outputs. See: #16

Fixes:
Sanity check for gff parsing that a identifier is present. See: #18

What's Changed

• PR by @jonas-fuchs in #17
• Full Changelog: v.0.7.1...v.0.7.2

v.0.7.1

What's Changed

• Added --reference by @jonas-fuchs in #15. This now allows to specify the ref id and generate plots for vcf with multiple refs, e.g. segmented viruses
• virHEAT ignores delete options if only one vcf is provided

Full Changelog: v.0.7...v.0.7.1

v.0.7

Update virHEAT to 0.7

New

• added -s --scores option that lets you link results from deep mutational screens to the heatmap
• added some more error catching
• added MAVE example data
• updated documentation

New Contributors

• @PlushZ made their first contribution in #13
  Thanks a lot! 💯

Full Changelog: v.0.6...v.0.7

v.0.6

NEW

• added --zoom option that allows to zoom into genomic region specified by start and stop values.
• added --name option that allows to customize the name of the plot and the file type. If none is given the default is still virHEAT_plot.pdf

FIXES

• Error catching if the gff3 is missing a region annotation (needed to get the correct genome length)
• small code structural changes

v.0.5.4

NEW:

• added the -n option that allows to delete mutations that appear in the heatmap n times or less. Will be applied after all filtering steps.

Example: -n 1 will delete all mutations indepent of their frequency if they appear only once in the heatmap. Particular helpful to declutter the heatmap and focus on specific mutations that e.g. appear and increase in frequency over time.

v.0.5.3

NEW:

• switched to store True for -a (now no comma sep is needed)
• check if array is empty (nothing to plot)
• changed the --delete rationale

Rationale: virheats --delete is primarily a tool to show how samples differ between each other while deleting mutations that are common to all samples. However, simply deleting the column of the array if all are greater than 0 might lead to misinterpretation. Now it only deletes if the frequencies do not differ more than 0.5. Thereby allowing to still visualize if a mutation is present e.g. an original sample in a low frequency which increases to a dominant mutation. Feedback is highly welcome here.

FIXES:

• fixed a bug where it would crash if all mutations lie outside annotations
• fixed a rare bug if INFO field contained "TYPE"

v.0.5.2

FIXES:

• incorrect requirements in setup.py and requirements.txt
• bug with plt.colorbar due to a newer version of matplotlib

v.0.5.1

FIXES:
fixed a bug for the coverage plot if positions are not in tsv (meaning cov = 0)

v.0.5

New:

• added support to read in per base coverages from qualimap. Allows to annotate samples where we do not find mutations but have also a coverage under a user defined threshold.