ShapeMapper2 version 2.2

• Added DMS mode option
• Fixed bug in MutationParser so that paired (unmerged) reads are now merged
• Provides a temporary fix to STAR mode so that it automatically runs in serial, avoiding the hang that happens in parallel
• Upversioned internal python and thirdparty codes:
  Pipeviewer 1.6.0 > 1.6.20
  Python 3.5.3 > 3.9.12
  numpy 1.11.3 > 1.19.5
  libgcc 5.2.0 > 7.2.0
  java-jdk 8.0.45 > 8.0.112
  perl-threaded 5.22.0 > 5.32.1
  scikit-learn=0.18.1 > 1.1.2
  matplotlib 1.5.1 > 3.6.2
  graphviz 2.38.0 > 7.1.0

ShapeMapper2 version 2.1.5

No future updates are planned beyond this final release.

Changes in this version:

• Fixed bug in reported median mutation rates in histogram figures
  (previous ShapeMapper versions actually displayed the 5th percentile)
• Added guidance for running ShapeMapper components piecemeal (see
  Modular workflow)
• Added output histogram plot of un-normalized ln(mut_rate_modified/mut_rate_untreated)
• Reorganized list of ShapeMapper dependencies (see Building)
• Adjusted --min-mutation-separation 0 behavior to match expectations
• Added missing --output-aligned-reads option
• Allow --input_is_unpaired argument to shapemapper_mutation_parser
  to override flags present in SAM alignment
• Fixed issue with unit test paths on machines outside the build environment
• Fixed issue with undocumented --separate-ambig-counts param
• Exposed bowtie2 effort params -R and -D as --max-reseed
  and --max-search-depth
• Added a more helpful error message in certain cases of missing input files
• Added error messages when attempting to run on a Mac or run when executables are not present
• Added a top-level CMakeLists to simplify most common build situation

ShapeMapper2 version 2.1.4

Changes in this version:

• Documentation reorganized and expanded
• Fix for crash with folder names shorter than 3 characters
• Amplicon primer pair mapping filters
• Now using paired-end alignment mode for paired reads that fail to merge
• Added test for overall pipeline accuracy on a small example dataset
• Added simplified reactivity profile outputs suitable for direct import into VARNA or Ribosketch (see
  Coloring by SHAPE reactivity).
• Refactored much of MutationCounter and MutationParser
  • Refactored Read class and used throughout
  • Moved all mutation processing and filtering functions from MutationCounter
    to MutationParser
  • Incorporated previously debug outputs into primary output of
    MutationParser
• Debug mutation rendering (--render-mutations) reworked
  • Provides more detailed information about each mutation
    processing step and quality filters
  • Outputs a multi-page pdf file scaled to fit the width specified
    by --max-paired-fragment-length
• Added end-to-end tests for unpaired inputs
• Bugfix for log file path when --name provided
• Exposed STAR --genomeSAindexNbase parameter
  • Added option to automatically rerun with defined --genomeSAindexNbase in the case of
    STAR segfault (see STAR parameters)
• Excluded lowercase sequence from mutation rate histogram plots
• Added --per-read-histograms option and disabled by default
• Print all subprocess stdout/stderrs to main log file if run failed
  and --verbose

ShapeMapper2 version 2.1.3

v2.1.3

first public commit