Metadata-Version: 2.1
Name: fdstools
Version: 1.2.1
Summary: Forensic DNA Sequencing Tools
Home-page: https://fdstools.nl
Author: Jerry Hoogenboom
Author-email: jerryhoogenboom@outlook.com
License: GPLv3+
Project-URL: Bug Tracker, https://github.com/Jerrythafast/FDSTools/issues
Project-URL: Source Code, https://github.com/Jerrythafast/FDSTools
Description: Forensic DNA Sequencing Tools
        =============================
        
        Tools for filtering and interpretation of Massively Parallel Sequencing data of
        forensic DNA samples. To obtain a list of included tools with a brief
        description of each tool, run:
        
            ``fdstools -h``
        
        For a complete description of a specific tool and its command line arguments,
        run:
        
            ``fdstools -h TOOLNAME``
        
        
        Installation
        ------------
        
        The recommended way to install FDSTools is by using the ``pip`` package
        installer. If you have ``pip`` installed, you can easily install FDSTools by
        typing:
        
            ``pip install -U fdstools``
        
        Alternatively, FDSTools can be installed by running:
        
            ``python setup.py install``
        
        
        Release Notes
        -------------
        v1.2.1 (2021-07-15)
            This release focuses on finishing support for Python2 before the transition
            to Python3. FDSTools will now display the help page if no command is given.
            A message about the transition to Python3 in the next version of FDSTools
            is added to the command-line help pages. Furthermore, dependency version
            numbers have been updated to ensure smooth installation on Python2 as well
            as a smooth transition to Python3.
        
        v1.2.0 (2019-03-29)
            Major improvements and fixes to the TSSV tool. Most notably, it no longer
            relies on the external ``tssvl`` program because that is no longer
            compatible with FDSTools. Furthermore, the new TSSV tool v2.0.0 comes with
            a major performance upgrade and has some updated command-line arguments.
        
            This release also fixes an issue in Samplestats and adds the ability to
            apply graph filtering before noise correction in Samplevis, making the
            effects of noise correction more apparent.
        
        v1.1.1 (2017-03-15)
            Fixeds incorrect calculation of tLeft, fLeft, rLeft, tRight and fRight
            columns in the report output file of TSSV, when -T/--num-threads was set to
            2 or higher. The primary output was unaffected.
        
        v1.1.0 (2017-03-14)
            In STR allele names for sequences that don't exactly match the description
            given in the library file, no more insertions are produced at the end of
            the prefix or the beginning of the suffix, in favour of extra STR blocks.
        
            Empty input files and broken pipelines are now handled gracefully across
            all tools. Specifically, an empty input file is now treated as if the
            expected columns existed, but no lines of actual data were present. This
            greatly helps in tracking down issues in pipelines involving multiple
            tools, as tools will now shutdown gracefully if an upstream tool fails to
            write output. Only the failing tool will output an error.
        
            Furthermore, a new option has been added to the TSSV tool, enabling
            multithreading support. This can greatly reduce analysis time by using
            more (or all) cores of the system's processor simultaneously.
        
            Finally, various small bugs and glitches were fixed.
        
        v1.0.1 (2016-12-21)
            FDSTools library files may now contain IUPAC ambiguous bases in the prefix
            prefix and suffix sequences of STR markers (except the first sequence, as
            it is used as the reference). Additionally, optional bases may be
            represented by lowercase letters.
        
            An option was added to the Pipeline tool to skip running Allelefinder,
            using a user-supplied allele list file instead. Multiple options have been
            added to the Vis tool and some have been regrouped to more easily find the
            option you are looking for.
        
            It is now possible to save the a Samplevis HTML visualisation after having
            made changes, preserving the changes made.
        
            And various minor bug fixes and improvements throughout.
        
        v1.0.0 (2016-10-03)
            Fixed an issue with variant descriptions in allele names of non-STR markers
            that made it impossible to convert those back to raw sequences.
        
            Added various useful options. Most notably, Samplevis now displays a
            tooltip when the mouse pointer is over an allele, providing various details
            about that allele.
        
            And various minor bug fixes.
        
        v0.0.5 (2016-09-06)
            Added the Library tool, for creating a template library file that includes
            helpful commentary and examples to get new users started. Creating an empty
            library file used to be a somewhat confusing option in the Libconvert tool.
            Also, the Blame tool was replaced with the more advanced BGAnalyse tool.
        
            Added the Pipeline tool, which implements some ready-made pipelines
            involving most of the other tools in FDSTools. Three pipelines are
            provided: one for noise reference sample analysis, one for case sample
            analysis, and one for generating a background noise database from the
            reference samples.
        
            In Samplestats, the default allele calling option thresholds have changed:
                - Changed default value of -m/--min-pct-of-max from 5.0 to 2.0
                - Changed default value of -p/--min-pct-of-sum from 3.0 to 1.5
        
            The TSSV tool was updated with an option to increase the panelty given to
            insertions and deletions in the flanking sequences. It now requires TSSV
            version 0.4.0 to be installed.
        
            Various upgrades to visualisations, bringing a new responsive design to all
            HTML visualisations and fixing various issues.
        
        v0.0.4 (2016-07-26)
            Improved debugging: FDSTools will now print profiling information to stdout
            when the -d/--debug option was specified. Also, all tools now correctly
            interpret '-' as the output filename as 'write to standard out'.
        
            BGEstimate has gained a new option to require a minimum number of unique
            genotypes in which a specific allele must have been seen before it will be
            considered for noise estimation. This is to avoid 'contamination' of the
            noise profile of one allele with the noise of another. If homozygous
            samples are available for an allele, this filter is not applied to that
            allele.
        
            Reduced the memory usage of BGPredict and BGMerge. Also, BGPredict will now
            output nonzero values below the threshold set by -n/--min-pct if the
            predicted noise ratio of the same stutter on the other strand is above the
            threshold. Previously, values below the threshold were clipped to zero,
            which may cause unnecessarily high strand bias in the predicted profile.
            Similarly, by default Stuttermodel will no longer output a fit on one
            strand if no fit could be optained on the other strand.
        
            Changes have been made to rounding and column order in Samplestats.
        
            Various minor fixes and enhancements have been made, mostly to the
            visualisations.
        
        v0.0.3 (2016-02-02)
            First version of FDSTools with all strings attached. Introduces 15 new tools
            and five visualisations.
        
            In Stuttermark, the column names 'name' and 'allele' have been changed to
            'marker' and 'sequence', respectively, reflecting those of all the other
            tools. WARNING: Stuttermark is now INCOMPATIBLE with output from TSSV, but
            made compatible with TSSV-Lite and the new, bundled TSSV tool instead.
        
        v0.0.2 (2015-07-23)
            Added a new global option: -d/--debug. This option disables the suppression
            of technical details that would normally be visible when an error occurs.
        
            Stuttermark now accepts raw sequences and allele names as input, which are
            automatically rewritten as TSSV-style sequences using a specified library
            file. Also, the 'name' column is now optional.
        
        v0.0.1 (2015-07-02)
            Initial version of FDSTools, featuring a single tool: Stuttermark v1.3.
        
Keywords: bioinformatics forensics stutter NGS MPS DNA sequencing STR
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Legal Industry
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=2.7.9, <3
Description-Content-Type: text/x-rst
