Merge pull request #8 from yoheirosen/master

Update Makefile with additional lib
Adding some gene annotations which should show up on the MHC assemblyhub.
Merge branch 'master' of github.com:adamnovak/sequence-graphs
Adding fake binary tree to appease hal2assemblyhub, and some munged Gencode genes with human-sensible names on refmhc coordinates.
Correcting some incorrect comments
Attempting to log coverage while building an index.
Successfully threaded minContext through, but actually using it causes a segfault. Needs debugging.
Fixed segfaults but minContext does not appear to be beinbg respected.
Added tests and solved problem of minimum context not being respected. Merged reference structure may have some errors from this bug.
Adding a new script to hopefully run MHCs in different orders
Actually starting jobTree going
Getting jobTree to integrate several runs' coverage statistics
Adding a final memory usage log from createIndex
Asking for more than 1 CPU since we start so many threads.
Adding alignment comparison. Not actually tested at all yet
Got it working just concatenating XML, now trying to get it to extract something meaningful from the XML.
Actually extract the right thing from the XML
Adding in the alt MHC alignments to version control, because writing a script to download them all seemed too complicated.
Making alignment comparison work when the alignments differ by not lettign rootSeq into the MAFs
Adding a script which is supposed to get and fix up the alt alignments