Changelog¶
Version 0.20.2¶
Informative error message if Gooey is not installed and
sm-analysis-guiis launched (issue #49).Wrong input partitions trigger error message (issue #12).
Version 0.20.0¶
Command line option to provide path to
ccsprogram.Fasta index is created for the original reference if it is missing (issue #55)
Removed runtime dependency on
setuptools(issue #81).
Version 0.19.0¶
sm-analysisfilters out molecules with subreads in only one strand (issue #77).blasrandccsoperations protected by sentinel to prevent that parallel computations overwrite the aligned/ccs files (iss. #64).Bug fixed in plot with rolling average of coverage
Issues: #58, #67
Added Unique ID to each line of output (issue #14)
Some improvements in the documentation.
The result of calling external tools is taken into account in the pipeline: to inform about a possible error and to omit a faulty molecule.
Version 0.18.0¶
Summary report for humans in HTML format with
plots, and
basic statistics about subreads, molecules, methylations, etc.
Issues: #59
Bugfixes: #61, #62, #65
Version 0.17.0¶
The molecules in the methylation report are the ones found in the aligned CCS file that pass all the filters (issue #43)
Circular alignment: it is assumed that the chromosome has a circular topology, which is taken into account in the analysis (issue #38)
bugfixes in _BamFilePysam: it was writing spurious newlines after the header and between lines in the body.
Other issues closed: #45, #54
Version 0.16.0¶
GUI for
sm-analysis:sm-analysis-guiAutomatic alignment of unaligned input BAM (issue #44)
Unpleasant error messages from Pysam suppressed (issue #46)
Consistent behavior of CCS step in
sm-analysis( issues #47 and #3)
Version 0.15.0¶
Calls to external tool
samtoolsreplaced by usage of thepysamlibraryIssues closed:
#10 (methylation report’s name shown on screen upon creation)
#27 (patitions taken into account in the methylation report)
#36 (a standard set of filters integrated into
sm-analysis)
Version 0.14.0¶
Issues #32 and #19 fixed
Added systematic documentation
Version 0.13.0¶
Methylation report V3, with
quality columns
length of (DNA) molecule
column with number of methylations
columns with number of subreads per strand per molecule
The list of molecules in a methylation report comes from the CCS file. Only molecules having the very same sequence in the reference and in the CCS are included.
Some improvements on the developmnet side:
code follows style guide (
flake8tests pass)pipelines ready
some issues fixed
Version 0.12.0¶
Added new command line options to
sm-analysis:-C|--aligned-CCS-bam-fileto pass an aligned ccs file (that file is used to produce the Methylation report)-c|--CCS-bam-fileto pass a ccs file (that file is used to produce the Methylation report, after being aligned, if the aligned version itself is not provided)--keep-temp-dirto preserve a copy of the temporary directory with all the intermediate files used in the process.-m|--modification-typesto select the modification types (m6A, m4C, …)--only-produce-methylation-reportto skip the analysis itself and only perform the last step: production of the methylation report.
Issue #2 closed
Version 0.11.0¶
Added option
-P|--partitiontosm-analysisto select what fraction of an input file must be processed. This change allows for an easy way to further parallelize the processing of input files within different nodes in a cluster.
Version 0.10.0¶
Bugfix in methylation report
New command line options for
sm-analysis:-N|--num-simultaneous-ipdsummarysto launch multiple instances of ipdSummary-n|--num-workers-per-ipdsummaryto use multiple workers within each instance of ipdSummary--nprocs-blasrto use multiple workers with blasr
Version 0.9.0¶
Methylation reports (output by
sm-analysis) conform now to V2 (see Description of data in the Methylation Reports).
Version 0.8.0¶
New command line options for
sm-analysisto choose the path to thealigner (option
-b|--blasr-path)indexer (option
-b|--blasr-path)ipdSummary (option
-i|--ipdsummary-path)
High level documentation about PacBio sequencing
Version 0.7.0¶
sm-analysisandbam-filterautomatically identify the structure of BAM file:where the molecule id is located (column)
sm-analysishas option to select the IPD model in ipdSummary (option-M|--ipd-model).
Version 0.6.0¶
added option
--versiontosm-analysisverbosity is configurable (cl option:
-v|--verbose)no tracebacks should reach the end user, only error messages
More user friendly output of
sm-analysis(with relevant key infos)
Version 0.5.0¶
Legacy code covered with tests: minimal
sm-analysisfunctionalityNew
csvoutput with methylation states per GATC
Version 0.4.0¶
Switched to Double-loop TDD approach
Code for
bam-filterre-organized and covered with tests (most of it)some bugs fixed
spike to parallelize (in node)
sm-analysis
History¶
0.1.0 (2020-04-30)¶
First release on PyPI.