add fastq interleaver script
Add IRC Channel to readme
Merge pull request #122 from genomebridge/irc-readme

Add IRC Channel to readme
Add design doc to CONTRIBUTING document
Merge pull request #125 from bigdatagenomics/matt-contribute

Add design doc to CONTRIBUTING document
Merge pull request #116 from jelson/fastq-interleaver

add fastq interleaver script
Adding InterleavedFastqInputFormat

- Handles reading a Fastq file which has paired reads in the same file
Modified pileup transforms to improve performance. Also, added options to specify whether reads at secondary alignments should be converted to pileups.
Merge pull request #129 from fnothaft/pileup-perf-and-options

Modified pileup transforms to improve performance + to add options
Update README.md

To improve the experience for users trying to build ADAM from source, I think it's worth explicitly adding the command to up the PermGen size and to turn off running tests, which should reduce the number of emails to the mailing list about failing builds and allow the new user to get moving with the jar file sooner rather than later.

Feel free to discard if you think either change does more harm than good.
Merge pull request #139 from hammer/patch-1

Update README.md
Update README.md

Change the remote URL to use HTTPS rather than SSH, as [GitHub recommends for users behind a firewall or proxy](https://help.github.com/articles/which-remote-url-should-i-use).
Merge pull request #140 from hammer/patch-2

Update README.md
Changing package declaration to match test file location and removing unused imports and unnecessary semicolons.
Merge pull request #143 from hammerlab/ifq-test-cleanup

Changing package declaration to match test file location and removing unused imports and unnecessary semicolons.
Merge branch 'master' of https://github.com/bigdatagenomics/adam into vcf-work-master-merge
Merge pull request #144 from nealsid/vcf-work-master-merge

Merge of last few days of work on master into this branch