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Created with Raphaël 2.2.027Mar2625241918177Jun423Oct2019181322Sep2128Jul27131287128Jun242217138210May9Apr2131Mar516Feb1529Jan2822201312710Dec723Nov161312929Oct282723201921Sep1730Aug2654331Jul168Jun429May30Apr29151097624Mar23181312109525Feb24191731Jan3029282724201613129813Dec418Nov151223Oct174330Sep252420Aug29Jul23221510May97630Apr218Mar27Feb2621198Jun31May3029161517Apr9Feb87131Jan3029fixed reading of data; previous modif was done too chicklymastermasterwork in progress: testing the impact of underlying buffer size when reading gzip fasta filesadded trace to have a n idea of the time needed to retrieve the number of reacors in the input fastq fileadded trace to get the number of lines in huge gzipped filevero_devvero_devadded trace to have a n idea of the time needed to retrieve the number of reacors in the input fastq fileadded a tool to get information about the fasta sequences when analysing a viromeMerge branch 'master' of https://gitlab.pasteur.fr/vlegrand/ptvfixed bug that caused checkpoint file to be generated several time in the same second. Now have millisecond precision to avoid teh problemfixed typowork in progress: better handling of checkpointsnext part of the fix for the same pb as the previous onefixed bug related to checkpoints (bad handling of the frequency)added the possibility to allow 1 mismatch in read seed mapping in functionnal parms and fixed unut testsadded missing dependency to regex moduleWant to test whether using regex module instead of re to allow 1 mismatch in the matching of the seed region impacts execution time.Merge branch 'master' of https://gitlab.pasteur.fr/vlegrand/ptvremoved dependency on deprecated sklearn packageput a more generic version number in Readme fileversion 4.3v4.3v4.3stable version 4.1.2fixed sequencefixed reference data for lamda phage since the bug impacted the rearranged sequence that served as reffixed typoadded new regression test for rearranged sequence and cohesive sequencefixed bug when rearranged sequence was not trimmedMerge branch 'master' of https://gitlab.pasteur.fr/vlegrand/ptvfixed old path to modulesUpdate .gitlab-ci.ymlupdated path of source module in broken testupdated path to source code modules in sh scriptsUpdate .gitlab-ci.ymlUpdate .gitlab-ci.ymlUpdate .gitlab-ci.ymlfinished packaging with poetryv4.2 ptv_packag…v4.2 ptv_packagingwork in progress for packaging phageterm with poetryadded gzip format support for genomeprocess_gzip_in…process_gzip_inputadded support for gzipped fileswork in progresswork in progresswork in progress for packaging and redistributing