Added support for fine mapping regions (fineMapPP and fineMapRegions)
Added support for GWAS catalog hits (gwas_hits)
Added control for # of rows for both of the above (fmrows and gwrows)
Removed space for title at top when title is not set
Reduced spacing between panels (was 0.5, now 0.25)
Removed debug comments
Fix which() not found issue
Changes to conf for latest 1000G LD and RSCRIPT_PATH
Fix for error message when tables do not exist
Added various tests
Fixed GWAS hits being 1 row too far down (and not showing up on the
plot)
Changed how finemapping credible SNP sets are plotted (points instead of
regions/ranges)
Added extra log pages at the end to list the GWAS hits and finemapping
regions (requires gridExtra to be installed)
New feature - conditional plots
Fix to gwas hits panel (was trying to use omitIdx when all rows could
fit)
Added ability to change conditional SNP plotting symbol (condRefsnpPch)
Added coloring all SNPs with LD in lowest bin the same color (condLdLow)
Can set conditional LD colors now (condLdColors)
Sets of conditional SNPs have their own unique symbols now (condPch)
Fixed SNPs to be plotted in order of highest LD (so SNPs with high LD
are plotted on top always)
Added drawMarkerNames to set whether rsID or chr:pos should be written
above the SNP
Refsnp line goes up to SNP symbol instead of text label now
Annotation key removed from 2nd page of PDF output if creating a
conditional LD plot
Bug fixes created from conditional plots
Added in support for calculating LD from VCF files (--ld-vcf)
Changed error message to be clearer when LD file directories could not
be accessed
Added a check to make sure VCF file has a tabix index when using
--ld-vcf
Added support for EPACTS results files (--epacts)
When using PLINK to calculate LD, LocusZoom will continue to create a
plot even if the marker does not exist within the genotype files
(previously it would just stop with an error, which was not consistent
with the original behvaior of new_fugue)
Added support for calculating D' from VCF files (requires phased VCFs)
Added general support for including "GWAS catalogs"
Fix for crash when no GWAS catalog specified
Updated test cases for new features
Additional tests for --ld-vcf and --gwas-cat
Better error message when PLINK or new_fugue cannot be found
Fixed test script to run in parallel using multiprocessing
Better error message if Rscript could not be located
Added support for marking individual markers on a plot (use
--denote-markers-file)
Re-arranged test cases to be able to load them individually
Fixed error with refsnp LD and conditional SNP LD overlapping
Fixed test script to only run 1 job per process (maxtasksperchild=1)
Better error messages for VCF parsing
Skip calculating LD from VCF file if problem with index SNP genotypes
Safer handling of LD cache when program terminates abnormally
Removed gz_read (deprecated for removal previously)
Changed --conditional to --add-refsnps (with backward compat for
--conditional)
Odds and ends for latest release