Update notes for WISARD version 1

Version 1.3 [top]

Version 1.3.2 (Sep 13, 2017)

• TBA

Version 1.1 [top]

Version 1.1.0.9 (November 18, 2014)

• TBA

• TBA

Version 1.1.0.8 (October 6, 2014)

• --corepacts added. Sample relatedness matrix can exported with EPACTS format and vice versa.
• WISARD now supports Solaris operating system. Compatible from Solaris 11
• Exclusion and inclusion options now mixed with --window option to broaden the affected range.
• Range type arguments now can use large number unit (kilo, mega and giga). See this section.
• FTP-related functions were added to WISARD.
• --markercheck and --markerupdate options were added. SNVs can be annotated with reference information.
• New two gene-level analysis for the family data, --pedgene and --famvt analyses were added.
• --regex added, filtering-related options can use simple regular expression.
• FQLS now can be applied to continuous phenotype.
• Redundant computation on FQLS was removed.
• The system now computes MAC only with all samples.
• Since FARVAT covers optimal statistic, it automatically activates --skato now.
• Some redundant output were removed.

• Bug on usage of <= or >= for ranged option was fixed.
• Chromosome counting bug on different species with --species option was fixed.
• Compilation bug on some cases on FreeBSD and Solaris was fixed.
• --misgeno now correctly applied with RAW file input.
• Redundant computation with --betaweight was fixed.
• Computation bug of --hmdr in some cases was fixed.
• Bugfix on --makegeno option.
• p-value computation failure on --vt in special cases was fixed.
• Wronly aligned output with --ld was fixed.
• Miswritten option descriptions were fixed.
• Bugfix of unexpected behavior with '--pname *' option.
• Redundant computation of minor allele frequency was fixed.
• Errornous behavior on --selfam with file argument was fixed.
• Error from bogus whitespace on the end of line in set file was fixed.
• p(1-p) type computation bug on some analyses was fixed.
• BIM file error on monotone variant export was fixed.
• Bogus character on SKAT-o output was removed.
• Rare bug on --simfreq was fixed.
• Unexpected behavior by --prevalence with continuous phenotype corrected.
• --regression bug on multi-thread was fixed.
• Multiple bugs on annotation were fixed.
• Several minor bugs were fixed.

Version 1.1.0.7 (July 28, 2014)

• --hethom added, het/hom ratio for each sample can be computed. (See here for use)
• --flip added, for genotype flip of entire dataset or subset.
• --varsubset added for the specification of --flip/--1234/--acgt option.
• --hmdr and subsequent options were updated. (See href for detail.)
• --hmdrprior and --hmdrall added for detailed HMDR manipulation.
• --setrandom added, for the generation of randomly generated gene mapping.
• --mdr now supports --perm to get permutation-based p-value.

• Rare failure on SKAT-o statistic computation was fixed.
• Rare matrix handling bug was resolved.
• Phenotype ignorance on LGEN format was fixed.
• HMDR no longer does redundant computation.
• Errornous default value on --setoverlap fixed.
• --miss reporting bug was fixed.
• Rare error on both FQLS and MFQLS was fixed.
• Overlapping of --randpheno/--randbinpheno was fixed.
• Memory leaks on several situation and analyses fixed.
• Some compilation bugs on several operating systems were fixed.

Version 1.1.0.6 (July 9, 2014)

• MQLS now can be separately performed with FQLS. (See here for example)
• --species added, other species' genetic data now can be processed with WISARD.
• --nodata added, analyses do not need genetic data itself can be executed with this option when there is no genetic data.
• --mdrthr added, MDR result can be filtered using this option based on the measure.

• Crashing bug fixed, when samples are resized with covariates assignment.
• Different column separator in --exportraw fixed. Now only uses single space.
• Memory leak bugfix on --longitudinal of --genetest.
• Bugfix in simplest genotype imputation, in special case.
• A bug on chromosome entry missing on HWE testing with single thread fixed.
• Q-test bugfix on Q3 p-value when Q1 and Q2 are extremely low.
• Possible memory bugs fixed.
• Duplicated computation of MAC was fixed to perform once.
• Loading bug on gene-marker mapping was fixed.
• Memory leaks on several situation and analyses fixed.
• Some compilation bugs on several operating systems were fixed.

Version 1.1.0.5 (June 25, 2014)

• --sampleweight added, Weighted Least Square (WLS) now can be used in --regression, only for continuous phenotype.
• --singleparent added, single-parent pedigree is now allowed in default but with this the restrction can be avoided.
• --nskip added, for the inputs, it is possible to skip the specific number of first n lines with this option.
• --lasso added, LASSO procedure now can be used accompanied by --regression, but now only capable to continuous phenotype.
• (Experimental) In order to strengthen family-based tests, FB-SKAT and rv-TDT were newly added.

• Some bugs on VCF file I/O were fixed.
• An unexpected behavior on the treatment on Minor Allele Count (MAC) fixed.
• A problem on --cor input not working properly with some from --corpair was fixed.
• Randomization algorithm replaced with advanced version.
• Some invalid setting on the compilation environment was fixed.
• Generating empty FAM file under --makevcf with specific condition was fixed.
• An unexpected behavior of --ref under specific condition was fixed.
• Some out-of-standard generation of VCF file was fixed.
• Unusual p-value reporting on gene-level test (Reports NA as negative value) was fixed.

Version 1.1.0.4