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 by pysam

[R03]

Add option --partition to sm-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, eg P6-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.