Added docs on makefiles and angsd
Fixed scale error in plotMetrics.R:dup() so that percentages are shown (0-100) rather than fractions (0-1)
Changed plotMetrics.R:hs() so that it runs even if flowcell IDs are missing in input
plotMetrics.R(): wrong name was used in call to hs() function
plotMetrics.R: numerous changes (layout changes to plots, and several new plots)
Added variable SPACE_CHAR in Makefile.general
Removed "-l INFO" from GATK_VARIANT_EVAL_OPTIONS in Makefile.gatk, so that GATK verbosity can be configured globally
Makefile.halo: Set read group platform unit (RPGU) to flowcell ID. For RealignerTargetCreator, added option -known providing raw variant calls, in accordance with pipeline presentation from Agilent. Removed -l from GATK_VARIANT_EVAL_OPTIONS so that verbosity can be set globally. Misc other fixes.
Updated Haloplex example Makefile based on a current makefile from an actual project
Misc small fixes to plotMetrics.R
Merge pull request #2 from pareng/master

Changes mostly to HaloPlex pipeline and plotMetrics.R
samtools: Add rules for various samtools commands

Add a shebang line, and make the script executable.
Merge pull request #3 from sjackman/samtools

samtools: Add rules for various samtools commands
Merge branch 'master', remote branch 'origin/master'
Merge branch 'master' into develop