First version of the chimera mapping pipeline
V0.0.2. Added three additional optional parameters to be set by the user: Max read length, Splice site consensus and Minimum split size.
V0.1.0 Produce just one output (not one for exotic and another one for normal). Merging at the level of echo the paths of the .gff.gz files into a single text file and give this file as input to chimsplice)
V0.1.1 Enabled log level options. Now it also displays information regarding the configuration of the chimera mapping and blueprint pipelines
V0.1.2 Putting under version control all the programs the pipeline depend on. Changed the paths for this programs
Added Sarahs script make_chimeric_junction_matrix.sh to the git tracking system
V0.2.0 The step of chimsplice where the strand of the split-mapping is rewritten correctly was moved from chimsplice to the steps 4 and 5 of the pipeline. Put under version control more programs the pipeline depend on.
V0.2.1 Fixed a bug in Gem2Gff.awk when compute the coordinates of the splitmappings in the gff. Changes done according to Paolo's indications.
V0.3.0  For the exotic mappings, now it reverses the blocks when the split-mapping are in the same chr, same strand and in the - strand. This is to write the split-mappings ordered according the convention of the bam (Genomic order)
V0.3.1 Now, the experiment identifier is a compulsory argument. Done to avoid user's mistakes.
V0.3.2 The input must be the mate's one FASTQ file and his name must end with _1.fastq.gz. Done to prevent user mistakes.
V0.3.3 Now more modular by looking at the presence of a file to do or not the step that produces this file
V0.3.4Latest version of the gemtools (/software/rg/el6.3/gemtools-1.7.1-i3) for the rna-pipeline step. Now, it stops and raises an error message if the output of one step is not produced. It also displays more information regarding the workflow
V0.4.0  Changed the way it computes the junctions and the total number of reads supporting each junction. It also provides the maximum beginning and end for each junction in the output matrices.
V0.4.1 Little modifications in the help and experiment replaced by sample in file names.
V0.4.5 Additional information for each chimeric junction in the output matrix: id, name, biotype of genes overlapping each part junction; information regarding if both part of the junction are in the same chromosome, if they are in genomic order and the distance between them and the ids and names where each part overlap.
V0.4.6 Added a comment in the help to tell the user that the pipeline run by default in unstranded mode. It checks if the file exon to exon connection file exists and skip the step in case yes.
V0.5.0 Additional step to compute the junction's canonical splice sites GT-AG or GC-AG, add this information to the matrix and for unstranded data write the junctions in biological order and add the strand to each part of the junction whenever it is possible.
V0.5.1 Improved the script to complete the chimeric junction matrix with information regarding the genomic position of the parts of the junctions. Now chimsplice can take gff annotation files with at least exon rows associated to their gene id in column 10 file and produce a correct matrix (It is not mandatory it has the gene name and the biotype as before).
Reorganized the project structure. Some files where renamed, moved, new directory organization