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

0.20.0

  • [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)

0.21.0

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

0.22.0

  • [R25] Documentation (II)

    • local distribution and installation of docs

    • launch local docs in browser

    • tutorial

    • structural refinaments

    • man page

1.0.0

  • [R16] Transparent usage of clusters. (?)

  • [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.

  • Issues & bugs

1.1.0

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

1.2.0

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

Past

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