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Created with Raphaël 2.2.07May30Apr24171028Mar1211717Feb149Jan12Dec10Oct15Jun25Jul31May249876543229Apr28151210Mar24Jan20191276517Dec1095Sep131Aug2625232031May27262522121110729Apr282726232221201916151312987629Jun1620Apr19141114Mar9Jan616Dec12Aug28Jul14110Jun331May272624231918171312229Apr1912116524Mar2322181715141110821Feb1918108526Jan1911868Dec18NovWe need to re read the score and not only the sequence when filling the filter because there is an option that replaces a nucleotide by N when its score is below a given threshold; Thsi avoid skiping kmers containing such nucleotides; now take that into account when computing maximum read length.dev_nanoporedev_nanoporework in progress : now get max value for useful read length amongst all processed filesadded test case for useful_read_length of PE reads and fixed bugupdated testfixed teh calculation of maximum useful read length; must now fix the previous testMerge branch 'dev_nanopore' of https://gitlab.pasteur.fr/vlegrand/ROCK into dev_nanoporework in progress: getting the maximum useful read lengthfixed compilation errorMerge branch 'dev_nanopore' of https://gitlab.pasteur.fr/vlegrand/ROCK into dev_nanoporework in progress; Investigating why it is so slow.added traces from benchmarkadded destructor for Filter classfixed bug : memory deallocation of cur_fq_record. TODO : take some time to make something cleaner on this topicmoved declaration of variable that allocates memory outside of for loopwork in progress for the handling of nanopore sequencing data. Still have to do higher level testingwork in progress in order to be able to process fastq files from nanopore sequencing.finalizing things for version 2.1v_2.1 masterv_2.1 masterremoved DEBUG tracesfixed bug related to output value of lseek that happened only on very large filesMerge branch 'master' of https://gitlab.pasteur.fr/vlegrand/ROCKfixed bug related to output value of lseek that happened only on very large filesUpdate CitationsUpdate run_tests_ci.sh, fixed typoUpdate .gitlab-ci.yml file; now using a redhat 8.8 image for CI.redhat 8.8 container for CInew script fr running tests in a docker containerfixed bug in testUpdate README.mdUpdating README.mdupdated manV_2.0V_2.0updated NEWSremoved unuseful comments and unuseful filesremoved unuseful use of unused argument MEM_CHECKUpdate README.mdUpdate README.mdUpdate paper.mdUpdate paper.mdUpdate paper.mdUpdate paper.mdUpdate paper.md