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¶
1.3.0¶
[R31] Switching to using the
pbmm2
aligner by default, allowing the usage ofblasr
if needed.
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¶
1.2.0¶
[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 bypysam
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
tosm-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¶
[R19] Methylation state conforms to version 2 (see Methylation Reports).
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 codeuse the FTs to define what the code does, and
cover the existing code with UTs