sets the new directory hierarchy: src, lib, include, bin
addes new file hierarchy for the hpg-aligner application: src, lib, include...
skip
skip
resolves conflicts with hmartinez
resolves first conflicts integrating hmartinezs code
compile, compile...but does it work?
Modifications for run RNA-Seq
fixes some bugs
Merge branch 'integration' of repos.bioinfo.cipf.es:hpg/hpg-aligner into integration
deletes lib/bioinfo-libs-module
Add new process for reporting splice junctions
cleans some code
removes submodules
updates Makefile
adds some external libraries
Maximum number of characters in one line resolved
adds pairend and mate-pair support
removes tmp files
adds support for pair reads