gatk3的最后一个经典版本3.8

Khalid Shakir c08468eb9d A couple of updates while trying to get desired R 2.13 compactPDF support. ... preQC: - For R 2.13 when parsing fingerprints explicitly coercing the text before parsing - Added LOD geom_line() at +/-3 based on Tim's presentation at PM meeting (ppt to go to pipeline wiki asap) - PF_INDEL_RATE of zero replaced with NA - NA's are not "violations" auto filter samples since 0+NA = NA, and subset test only looks for 0 violations - Restored plots for MEAN_READ_LENGTH, BAD_CYCLES, and MEDIAN_INSERT_SIZE by explicitly print()'ing the created plots postQC: - Fixed R 2.13 font scaling by moving size out of aes, except when using highlighting - TODO: Don't know how to scale by aes for highlighting *and* use a smaller overall font size outside aes		2011-09-29 11:21:50 -04:00
public	Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-09-28 18:17:34 -04:00
settings	Merged bug fix from Stable into Unstable	2011-09-27 14:34:39 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	To work around potential problem with invalid javax.mail 1.4.1 in ivy cache, added explicit javax.mail 1.4.4 along with build.xml code to remove 1.4.1.	2011-09-20 00:14:35 -04:00
ivy.xml	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00