use canonical representation of strings for some input command syntax in pipeline

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2433 bfd2a824-b778-4082-b236-bff916e0c2bb
add dot plot to plot_fields

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2434 bfd2a824-b778-4082-b236-bff916e0c2bb
add KING pipeline

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2435 bfd2a824-b778-4082-b236-bff916e0c2bb
add a utility function to convert double quote to single quote; applied to pipeline and vtools_report

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2436 bfd2a824-b778-4082-b236-bff916e0c2bb
correct the previously uploaded wrong KING.pipeline file ... 

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2437 bfd2a824-b778-4082-b236-bff916e0c2bb
Add function maf() to command vtools update --from_stat, pending testing

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2438 bfd2a824-b778-4082-b236-bff916e0c2bb
improve convertQuote() function

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2439 bfd2a824-b778-4082-b236-bff916e0c2bb
minor fixes to previous two revisions

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2440 bfd2a824-b778-4082-b236-bff916e0c2bb
Fix track() function for online vcf files (the code allows multiple local files but disabled online track)

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2441 bfd2a824-b778-4082-b236-bff916e0c2bb
Add a bunch of warning messages for numerator > denominator during the calculation of MAF

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2442 bfd2a824-b778-4082-b236-bff916e0c2bb
Exclude variants from pseudo-autosomal regions on chromosome X and Y so that they could be treated as autosome during te calculation of MAF

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2443 bfd2a824-b778-4082-b236-bff916e0c2bb
add XY positions for hg18

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2444 bfd2a824-b778-4082-b236-bff916e0c2bb
Fix syntax error for previous patch

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2445 bfd2a824-b778-4082-b236-bff916e0c2bb
Computation of inbreeding coef roughly complete

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2446 bfd2a824-b778-4082-b236-bff916e0c2bb
add build info to inbreeding coef function

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2447 bfd2a824-b778-4082-b236-bff916e0c2bb
Update bwa pipeline to remove dumped fastq file after .sam file has been created (production mode only).

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2448 bfd2a824-b778-4082-b236-bff916e0c2bb
finish up calculation of inbreeding coef

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2449 bfd2a824-b778-4082-b236-bff916e0c2bb
Add vtools admin --validate_sex

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2450 bfd2a824-b778-4082-b236-bff916e0c2bb
Minor update to the previous patch: allow missing values for validate_sex, display number of variants on pseudo-autosomal regions.

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2451 bfd2a824-b778-4082-b236-bff916e0c2bb
fix previous patch to use correct position to compare with pseudo-autosomal region

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2452 bfd2a824-b778-4082-b236-bff916e0c2bb