Update thousand genomes annotation database to fix an error (wrong GMAF field) in the previous version

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2488 bfd2a824-b778-4082-b236-bff916e0c2bb
Update thousand genomes annotation database to fix an error (wrong GMAF field) in the previous version

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2489 bfd2a824-b778-4082-b236-bff916e0c2bb
Minor fix to automatically generated .fmt files (for field alt)

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2490 bfd2a824-b778-4082-b236-bff916e0c2bb
Modify the import_vcf pipeline to make the output .fmt file optional

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2491 bfd2a824-b778-4082-b236-bff916e0c2bb
Remove several fields that are all missing from thousandgenomes

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2492 bfd2a824-b778-4082-b236-bff916e0c2bb
Remove an empty database if the creation of annotation database is interrupted.

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2493 bfd2a824-b778-4082-b236-bff916e0c2bb
More debugging messages etc.

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2494 bfd2a824-b778-4082-b236-bff916e0c2bb
Revert part of a previous patch because attching an non-existence annotation database has been used to create genotype databases

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2495 bfd2a824-b778-4082-b236-bff916e0c2bb
Do not stop if genotypes cannot be removed from a sample (a warning is given)

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2496 bfd2a824-b778-4082-b236-bff916e0c2bb
Separate local and online snapshots for the output of vtools show snapshots

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2497 bfd2a824-b778-4082-b236-bff916e0c2bb
Add parameter limit to bam track to limit the number of reads, calls, scores to display when the depth of coverage is high

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2498 bfd2a824-b778-4082-b236-bff916e0c2bb
Add parameter strand to limit the output of bam track for the track() function to specific strand (+ or -)

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2499 bfd2a824-b778-4082-b236-bff916e0c2bb
Allow the change of delimiter of the output of track() function through parameter delimiter

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2500 bfd2a824-b778-4082-b236-bff916e0c2bb
Try to identify the wrongly-specified field and give a more accurate error message after the command vtools output fails

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2501 bfd2a824-b778-4082-b236-bff916e0c2bb
Add parameter type, strand and show_seq to the bam track() function to better output reads information for different types of reads. This patch also changes how reads are displayed to match more of the samtools/tview output

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2502 bfd2a824-b778-4082-b236-bff916e0c2bb
Display insertions as I in the calls output of bam track() function

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2503 bfd2a824-b778-4082-b236-bff916e0c2bb
Fix field REF_FREQ_INFO in thousand genomes annotation database

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2504 bfd2a824-b778-4082-b236-bff916e0c2bb
allow for alternative field name be input genotype in association tests (for example genotype dosage)

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2505 bfd2a824-b778-4082-b236-bff916e0c2bb
adjust test data to match the updated weighting behavior with missing values

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2506 bfd2a824-b778-4082-b236-bff916e0c2bb
Merge remote-tracking branch 'upstream'

Conflicts:
	annotation/thousandGenomes.ann