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File Release Notes and Changelog

Release Name: 1.2.2

Release Notes
New release of CRAC v1.2.2:

- Correction of bug #15576 with mandatory arguments between --server and -o arguments
- COrrection of bug #15575 with segfault using -k argument
- Correction of bug #15540 (memory leak with deletions in sequence errors) 
- Correction of the bug #15352 that was due to a bad merge between 2097 and 2114 revisions of taginfo.cpp file.
- Correction of the Kmer verification test for paired reads and chimera.
- Correction of bug #15579 (only show once support and localisation when --detailed-sam)
- Correct the samOutput for paired-end reads. The field Rnext was not properly filled and the flag was update with paired-end data after being written.
- Correct a segfault when using option --splice. We were trying to write in spliceNoCover as well.
- Add a --no-ambiguity option in crac.cpp to increase accuracy in exchange for sensitivity
- Add a new output file "pairedEndChimera", this file contains chimera between paired-end tags where junctions are not sequenced. A new parameter to use this file is available : --paired-end-chimera.
- Add some unit tests for chimeras, the CIGAR chaine, SNVs
- Repetition: correct a bug and change condition to save the longest repetition
- Change packaging to take account of the man page
- Set cigar to * in sam when segment is unmapped
- Update the text to display when using --version option
- CRAC -emt: correct bug -> reverse the profile and localisation in detailed-sam output when read is reversed.