Requirements¶
A list of features to be added to the package. Requirements marked with (*)
are not yet assigned a version number.
- [R01]
bam-filter
covered with tests- [R02]
samtools
replaced bypysam
- [R03]
Add option
--partition
tosm-analysis
to select what fraction of an input file must be processed- [R04]
Implement new
csv
output with methilation state per molecule and circular consensus DNA sequence- [R05]
Option to select model in
sm-analysis
(simply providing a string, egP6-C4
). Instead of crashing if the expected model dows not agree with the chemistry, the program looks for different models in the directory and tests them in turn until a valid one is found.- [R06]
Legacy code covered with tests: minimal
sm-analysis
functionality- [R07]
Optimization: Reduce the number of temporary files that are created by
sm-analysis
.- [R08]
Decouple from ipdSummary using kineticsTools as a package
- [R09]
Automatically identify structure of BAM file:
where the molecule id is located (column)
- [R10]
BAM files created contain info about source file and modifications introduced.
- [R11]
Miscelaneous improvements:
protection against tracebacks (they should not be presented to end user)
version
debugging
- [R12]
Path to external tools can be provided:
blasr
pbindex
ipdSummary
- [R13]
Number of processes used by external tools can be chosen.
- [R14]
Resume interrupted
sm-analysis
runs.- [R15]
Various minor input options:
modification types
keep temporary directory?
only produce methylation report
ccs file
aligned ccs file
- [R16]
(*)
Transparent usage of clusters.
- [R17]
GUI
- [R18]
Easy installation
- [R19]
Methylation state conforms to version 2 (see Methylation Reports).
- [R20]
Documentation (I)
Structure documentation
Add quick start and some more docs for end users
add docstrings as a starting point for docs for developers
integrate with sphinx
- [R21]
Methylation report format V3
- [R22]
Summary doc for humans (html?, pdf?) with:
plots
basic statistics about subreads, molecules, methylations, etc.
- [R23]
New option that disables the standard filters before running the Single Molecule Analysis (
sm-analysis
)- [R24]
Path to
ccs
can be provided as CLO.- [R25]
Documentation (II)
local distribution and installation of docs
launch local docs in browser
- [R26]
BamFile implementation using pure python library
pybam
(or a python3 compliant fork of it)- [R27]
Organization of files produced by
sm-analysis
:log files go to a dedicated
log/
directory (each molecule must have its onw log file)auxiliary files (
ì-shifted...
, aligned BAMs, CCS, etc) must go into a dedicated directory (aux/
?)
- [R28]
Browsable HTML document with information about status of individual GATCs and the neighbours.
- [R29]
Automatic merge of partition results
- [R30]
Option to choose the window of the reference to be processed by
ipdSummary
.- [R31]
Switching to use the
pbmm2
aligner by default.