Roadmap

The roadmap is a summary of planned changes. It is splitted into two parts:

The difference between Past and the Changelog is the point of view: Changelog is intended for end users whereas Past is mainly for developers.

Future

1.4.0

  • [R23] New option that disables the standard filters before running the Single Molecule Analysis (sm-analysis)

  • [R30] Option to choose the window of the reference to be processed by ipdSummary.

1.5.0

  • [R14] Resume interrupted sm-analysis runs.

    • can provide the name of the temporary directory

    • can identify what molecules have been already processed and skips them (issue #17)

1.6.0

  • [R08] Decouple from ipdSummary using kineticsTools as a package (?)

  • [R26] BamFile implementation using pure python library pybam (or a python3 compliant fork of it)

  • [R10] BAM files created contain info about source file and modifications introduced.

1.5.0

  • [R18] Easy installation (after [R26])

Past

1.3.0

  • [R31] Switching to using the pbmm2 aligner by default, allowing the usage of blasr if needed.

  • New mechanism to choose the minimum mapping quality in the filters applied by sm-analysis to the input BAM. It defaults to an estimation of half the maximum value of the mapping quality found in the aligned file, but it can be manually set using the --mapping-quality-threshold command line option.

  • The SummaryReport includes statistics of mapping quality in the aligned BAM as well as a histogram.

1.2.0

  • [R29] Automatic merge of partition results

1.1.0

  • sm-analysis program analyzes each molecule using a window for the reference (issue #91)

  • Other performance improvements: issue #51 (optimal processing of BAM files not sorted by molecule id), #101 (slow seaborn plot).

  • Some fixes in the docs.

  • Other issues: #100 (Makefile), #106 (BAM files with variable number of columns),

1.0.0

  • [R25] Documentation (II)

    • local distribution and installation of docs

    • launch local docs in browser

    • tutorial

    • structural refinaments

    • man page

  • Issues & bugs

0.20.0

  • [R24] Path to ccs can be provided as CLO.

  • Issues: #55, #81

0.19.0

  • Issues: #14, #15, #58, #64, #67, #77

0.18.0

  • [R22] Summary doc for humans (in HTML) with:

    • plots

    • basic statistics about subreads, molecules, methylations, etc.

  • Issues: #59, #61, #62

0.17.0

  • Issues: #43, #38, #54, #45

0.16.0

  • [R17] GUI

  • Issues: #44, #46, #47, #3

0.15.0

  • [R02] samtools replaced by pysam

  • merge to master branch

  • Issues #10, #27 and #36 fixed

0.14.0

  • Issue #19

  • [R20] Documentation.

    • Structure documentation

    • Add quick start and some more docs for end users

    • add docstrings as a starting point of docs for developers

    • integrate with sphinx

0.13.0

  • [R21] Methylation report format V3

  • pipelines (?)

  • Issue #16, #28, #29, #5

  • Code follows style guide (flake8)

0.12.0

  • [R15] Various minor input options:

    • modification types

    • keep temporary directory

    • only produce methylation report

    • ccs file

    • aligned ccs file

  • Issue #2

0.11.0

  • [R03] Add option --partition to sm-analysis to select what fraction of an input file must be processed

0.10.0

  • [R13] Number of processes used by external tools can be chosen.

0.9.0

0.8.0

  • [R12] Path to external tools can be provided:

    • blasr

    • pbindex

    • ipdSummary

0.7.0

  • [R09] Automatically identify structure of BAM file:

    • where the molecule id is located (column)

  • [R05] Option to select model in sm-analysis

0.6.0

Miscelaneous improvements:

  • protection against tracebacks (they should not be presented to end user)

  • version

  • debugging messages

  • More user friendly output of sm-analysis (with relevant key infos)

0.5.0

  • [R06] legacy code covered with tests: minimal sm-analysis functionality

  • [R04] Implement new csv output with methilation state per molecule and circular consensus DNA sequence

0.4.0

  • [R01] bam-filter: convert legacy code into production code

    • use the FTs to define what the code does, and

    • cover the existing code with UTs