minor changes
Merge branch 'master' into junction
fixed bug in regions exceeding chromosome ends
first working version re-implemented junctions remapping
debugged junction remapping, included junction tolerance, added new parameter JI - number of introns for junction remapping
enabled multi threading by copying junctions into combinations, not blocking the lock too long
fixed bug in junction remapping, where pointer decrement caused address violation
minor change in cutoff for no. of combinations
improved debug output
merged master into junction
Merge branch 'master' into junction
fixed bug in junction remapping, occuring when blocks exceed the chromosome boundaries
minor change in config description. renamed old option
changed version
deleted test file
fixed bug in IUPAC ambiguity code handling for alignments on the reverse strand
Merge branch 'master' of git.ratschlab.org:software/palmapper
changed junction map locking
adapted printed messages to the new index versions
resolved conflict after merged in branch junction