completed single covariate tests by implementing all the interfaces; will work on interface for generalized weighted sum burden test next

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1294 bfd2a824-b778-4082-b236-bff916e0c2bb
adjusting phenotype classification criteria to allow for quantitative traits

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1295 bfd2a824-b778-4082-b236-bff916e0c2bb
framework for generalized weighted genotype burdent tests

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1296 bfd2a824-b778-4082-b236-bff916e0c2bb
completed interface and implementation for generalized weighted genotype burden methods. Pending for tests on real data

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1297 bfd2a824-b778-4082-b236-bff916e0c2bb
minor typo fix

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1298 bfd2a824-b778-4082-b236-bff916e0c2bb
small fixes; more exception handling

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1299 bfd2a824-b778-4082-b236-bff916e0c2bb
fix bug due to the use of cmath 'abs' (should use fabs or std::abs ...)

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1300 bfd2a824-b778-4082-b236-bff916e0c2bb
re-implementation 2 by 2 table exact test method

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1301 bfd2a824-b778-4082-b236-bff916e0c2bb
format c++ codes && add pyper.py to prepare for calling R from python via pipe

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1302 bfd2a824-b778-4082-b236-bff916e0c2bb
SKAT interface

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1303 bfd2a824-b778-4082-b236-bff916e0c2bb
Change the default behavior of vtools show (display all records) and unified the usage of --limit in commands show and output

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1304 bfd2a824-b778-4082-b236-bff916e0c2bb
completed the SKAT interface

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1305 bfd2a824-b778-4082-b236-bff916e0c2bb
Fix an error for args.limit is None

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1306 bfd2a824-b778-4082-b236-bff916e0c2bb
Output number of failed items in the progress bar

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1307 bfd2a824-b778-4082-b236-bff916e0c2bb
updated progress bar for association tests to use colored symbols for failure

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1308 bfd2a824-b778-4082-b236-bff916e0c2bb
Fix colored (red for error) progress bar

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1309 bfd2a824-b778-4082-b236-bff916e0c2bb
Forcefully remove .proj and .DB files if a project fails to open due to, for example, malformed database

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1310 bfd2a824-b778-4082-b236-bff916e0c2bb
Make sure loadProperty and saveProperty return the default value instead of raising an exception when error happens. This simplies the logic when these functions are used

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1311 bfd2a824-b778-4082-b236-bff916e0c2bb
Fix done() status line for ProgressBar

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1312 bfd2a824-b778-4082-b236-bff916e0c2bb
Run pragma for each attached database before pragmas such as cache_size needs to be repeated for each attached database

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@1313 bfd2a824-b778-4082-b236-bff916e0c2bb