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Created with Raphaël 2.2.025Feb201913Dec9Aug16Dec1Sep25Aug181618Mar1716151020Jan1916Dec15109612Nov21OctUpdate README.mdmainmainUpdate README.mdUpdate README.mdUpdate README.mdUpdate includes in Traceback.hMaking minimum length requirement of reads in crop_unmapped after base quality trimming a parameter.Adding option for setting the minimum base qualities of reads to be cropped for unmapped assembly.Adding total read count in BAM file to POPINS_SAMPLE_INFO file instead of command line.Adding total read count in BAM file to command line output.Fixing Nat Genet referenceand link to journal in README.md.Simplifying dependency on Bifrost installation.More edits to README - command descriptions still incomplete.Updating version information.Edited README - command descriptions still incomplete.Adding back an option to suppress printing the POPINS_SAMPLE_INFO file.Replacing popins2 by popins4snake in status messages.Cleaning popins4snake code, in particular the argument parser. Introducing a merge-locations command by splitting this task from place-refalign.Removing .gitignore from .gitignore.Adding .gitignore file.Cleaning unused PopIns2 leftovers from popins4snake code.Merge branch 'fix-sam-format-PG-IDs' into 'main'fixed duplication issue in PG ID fieldsfix-sam-format-…fix-sam-format-PG-IDsfix atoi, as it's not part of gccMerge branch 'fix-sam-format-PG-IDs' of https://gitlab.informatik.hu-berlin.de/fonda_a6/popins4snake into fix-sam-format-PG-IDsupdate PG IDs fieldsMerge branch 'main' into 'fix-sam-format-PG-IDs'improved conflict solving for duplicated PG IDs when merging SAM headersMerge branch 'fix-find-locations-io' into 'main'fixing file existence checkMerge branch 'fix-find-locations-io' into 'main'add IO of non-ref alignment file nameinitial change to see if SAM/BAM headers are modifiedMerge branch 'fix-crop-unmapped-io' into 'main'crop-unmapped with even more flexibility of the input parameters, se, pe1, pe2Merge branch 'fix-crop-unmapped-io' into 'main'new I/O for the crop-unmapped modulefix conflict after mergeMerge branch 'main' of https://gitlab.informatik.hu-berlin.de/fonda_a6/popins4snake into mainMerge branch 'new-find-locations-module' into 'main'new find-locations module