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 ofblasr
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 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