sample_stat: Move warning message before calculating anything to avoid disrupting progress bar

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@532 d9dedb58-ee9f-4e25-a36f-69be828a56f2
sample_stat: handle the case of mismatch type better. Send a summary statistics of variants updated

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@533 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Fix sample_stat for the handling of NULL records

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@534 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Do not use option geno because there is no alternative to set

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@535 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Shorten names in show format FORMAT to make it more consistent with terms used in other places

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@536 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Fix TestInit.TestParent

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@537 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Make most tests in test_import.py work

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@538 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Keep updating other samples if vtools phneotype --eset fails for one sample, fix test_phenotype

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@539 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Fix test_sample_stat

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@540 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Fix test_sample_stat for python 3

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@541 d9dedb58-ee9f-4e25-a36f-69be828a56f2
All tests run now, taking 200s on my machine. Hopefully gao can get similar performance on his new machine

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@542 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Releasing 1.0rc1

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@543 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Find an instance of non-unique index, need to figure out how this happened.

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@546 d9dedb58-ee9f-4e25-a36f-69be828a56f2
name changes in DP, etc.

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@547 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Trying to fix the uniqueness problem with the primary reference genome when multiple variants in reference genome are mapped to the same coordinates in primary referene genome

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@548 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Remove filename entry if all its samples have been removed

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@549 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Remove alternative reference genome if alt_? fields are removed

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@550 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Add a function to check the integrity of project when it is opened. This might bite us but can help identify bugs

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@551 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Fix a typo

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@552 d9dedb58-ee9f-4e25-a36f-69be828a56f2
Minor improvements on progress bar, count etc

git-svn-id: https://varianttools.svn.sourceforge.net/svnroot/varianttools/trunk@553 d9dedb58-ee9f-4e25-a36f-69be828a56f2