- Added a new rule to the Makefile to be executed without compiling all the dependencies

- Added a README file
Filtering module:

- Implemented an awk script to filter the chimeric junction candidates according
a filtering criteria set by the user (nb. staggered, nb. encompassing pairs and
similarity information between connected gene pairs)
Filtering module:

- Added some comments to the code
Filtering module:

- Added as a new step in the main script, ChimPipe.sh.
- Now the user has a new option -F to set the configuration of the
filtering module.
- If not set it uses a default configuration.

Log:

- Added \n at the end of each error message.
getopt:

- Substituted getopts by getopt in order to have long options.
- Added getopt code and binaries to the tracking system, since it is
not available in all linux distributions.
Display usage message when error in checking input variables
Help:
- Reorganized help text.
- Added long options to the help.
Help: removed a chunk of code that was copy by mistake
Check user´s input:
- Improved a lot. Now checks if the content of every input variable is ok
exiting and raising and error otherwhise
help:
- Substituted ChimPipe.sh by $0.
Help:
- Little changes in the description of the option --filter-chimeras
Reversing blocks in the -/- and same chromosome:
- Before reversing the ones coming from the second mapping and now reversing the ones from the first mapping instead
- Done to have all the blocks (first/second mapping) in the same orientation and to have the consensus splice
sites in the same position for all of them.
Make chimeric junctions from staggered-splitmappings. Very big changes, completely recoded since we
were computing them in the wrong way. These are the main ideas behind the changes:

- Determining the block strandedness for unstranded data. Before we were looking at the consensus splice site (css)
sequence and considering they map in the plus when they have css and in the minus when they have the reverse complementary
of the css. This was totally wrong, if they have the reverse complementary of the css means that what was sequenced was
the reverse complementary of the rna, so the trully strand is the opposite to the mapping strand.

- For stranded data the reads should always split-map with css and not with the reverse complementary sequence of the css.
However, these cases are produced by the mapper so we decided to filter out all this junctions in the step where we
make the junctions.

- Also changed the way the maximum beginnig and end are computed, since it was wrong.
Conversion from bam to gff. Important changes in order to generate a gff with all the blocks in the correct orientation
according to the strand:

- New awk script to convert the bed12 into bedPE. Needed since I need to swap the blocks when I change the mapping strand according to the sequencing
library for stranded data.

- New awk script to correct the mapping strand for the needed mate in the bedPE file and swap the blocks. I.E for MATE2_SENSE, if /1 maps in the +, the strand is
changed into - and the blocks are swapped to write them in the correct orientation.

- New awk script to convert bedPE into gff.
Conversion from gem second mapping file to gff. Changes in the script to correct the strand to put the blocks
in the correct orientation according to the strand:

- Modified the awk script to correct the mapping strand for the needed mate in the map file and swap the blocks. I.E for MATE2_SENSE, if /1 maps in the +, the strand is
changed into - and the blocks are swapped to write them in the correct orientation. This happend for all the possible mapping combinations (++,+-,-+,--)
Conversion from bam to gff. Error in the previous commit, I forgot to remove one line
Make chimeric Junctions. Fixed an error when declaring an awk variable, its name was wrong
Make chimeric junctions.

- Renamed the script staggered_to_juncion.awk.
- Added some documentation explaining how the script works.
Convert from bam and gem into gff. Added some documentation explaining how some of the scripts work.
Make chimeric junctions. Fixed an bug in the awk script to make the chimeric junctions:
- I was not renitializing the variables juncStr1, juncStr2, juncDonor and juncAcceptor. So in the case it did not find css for a junction
it was using the css and strand for the previous junction. What is totally wrong. Fixed by initializing this variables as empty variables
for each staggered in the function findStrand.
- It not css are detected rise an error and exit.