FIXED: check for emply line

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@677 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
UPDATE: added check on gene1 and gene2

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@678 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
added most of the code

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@679 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
UPDATE: removed the bowtie alignment step
revised the BLAT alignment with the use of fastx_collapser to speed up

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@680 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
FIXED: properly counting numInter, i.e. accounting for the spliced reads

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@681 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
UPDATE: added documentation, and minor fixes

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@682 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
UPDATE: added uthash.h gfrRandomPairingFilter sam2bp

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@683 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
UPDATE: checking only for DASPER < 1; added a HASH

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@684 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
UPDATE: added gfr2images gfr2bed

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@685 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
UPDATE: added documentation; checks on valid inter transcripts, compatibility of direction et al.

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@686 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
UPDATE: version number

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@687 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3
UPDATE: modified Doxigen instructions

git-svn-id: svn+ssh://svn.gersteinlab.org/repos/bioinfo/fusionSeq@688 2fd4de08-f6cc-4d2b-b124-baeea9ba92f3