bug fix get_default_alignment_results method
updated expected data

Updated several files expected outputs:
    genome-instrument-data-list2.out
    genome-model-clinseq-list1.out
    genome-model-clinseq-list3.out
    genome-model-rnaseq-list2.out

genome-instrument-data-list2.out was because insert size information was
added to the instrument data.  The other three are all related to
rebuilding of dependent builds due to some issue with the alignments
(tmooney handled that).
Merge branch 'master' of ssh://git/srv/git/genome
restore default_values

This tool is using defaults to find compatible models or creating new
models if needed (which would then validate their inputs as well).  So I
think it may be an exception to the "no defaults" rule.

That commit did not convert several defaults which possibly should have
been converted (if this is ever unreverted).

This reverts commit 935b04397f9b925fac4b80aacbdcbcf79d70dea8.
updated ur submodule to 318fcdc
updated jenkins submodule to 6fdbd47
updated jenkins submodule to bad136a
InstData Import Basic: convert format into original_format and import_format
InstData Import: rename basic test
InstData Import: mv bam test from fastq into separate file
InstData Import: mv fail tests from fastq into separate file
InstData Import: remove moved fail and bam tests from fastq
InstData Import: move flagstat into separate method
InstData Import: make method to verify and move bam
InstData Import: mv bam sort into separate method
InstData Import: Add SRA functionality
InstData Import: check ncbi config file
InstData import: only dump primary alignemnts from sra
reapply most of Gabe's commit to remove default_values

I mistakenly reverted a previous commit instead of only a couple files
in it. This reapplies the rest of the changes.

Erroneous Revert: 1da947a655ceb82bc450766333b21260ca20885d
Original Change: 935b04397f9b925fac4b80aacbdcbcf79d70dea8
update expected output

Updated `genome-model-rnaseq-list2.out` now that several builds have
completed so several columns are now filled in with values instead of
nulls.