Updated 0.4.0 release

This is identical to the 0.4.0 that many have been using, except it no longer run git submodule update virtualenv with --depth=1, since we have syncd that module from upstream.

0.3.0,

Falcon v0.3 Release Note

• Integrate latest (Apr. 2015) Gene Myers' daligner code
• Supporting read length up to 100kb from current 64kb
• New consensus code which process reads from diploid genomes better
• Logging for tracking job submission

Important changes

• It uses up-to-date Gene’s daligner code. It helps to support read > 64kb and helps for tracking read identifiers through the pipeline (which is important for diploid assembly in the future). The cost is that the new code use twice more memory if the daligner parameters is the same before. One needs to use the “-M” option to set limit on the memory usage. For human assembly, we tested with -M 32 for using 32G RAM for each daligner. Other possibilities are under investigation. (This is for pa_HPCdaligner_option and ovlp_HPCdaligner_option. See Wiki Manual for more details.)
• You will need a new option --output_dformat for the configuration variable falcon_sense_option. It is used in LA4Falcon and fc_consensus.py to generate p-read fasta files that are compatible to DAZZ_DB's fasta2DB for creating p-read database.