pygenclean - Version 1.8.3

This release fixes a small issue in the automatic report (missing value for HH missing at the moment of creation of the report).

- Python
Published by lemieuxl almost 9 years ago

pygenclean - Version 1.8.2

This release fixes a small issue in the automatic report (logic error for samples and markers missing rates in the summary result table).

- Python
Published by lemieuxl about 10 years ago

pygenclean - Version 1.8.1

This release fixes an issue with the installation.

- Python
Published by lemieuxl about 10 years ago

pygenclean - Version 1.8.0

Here are the changes for the 1.8.0 release: - It is now possible to estimate sample contamination using bafRegress. - Scree plot was too long in the automatic report; it has been reduced to fit the report page. - Only autosomes are used for creating genome file (IBS and MDS). - Better logging capability. - Updated documentation. - Correction of minor bugs.

- Python
Published by lemieuxl about 10 years ago

pygenclean - Version 1.7.1

These are the changes in the next release: - Improved content in the automatic report. - Improvement #7, where the list of significant markers for the plate bias step is no longer reported, but only the number of significant markers for each plate is. - Improvement #8, where the samples were sorted in the sex check step so that the order is consistent between the table and the different figures (if any). - Improvement #9, where a table summarizing the status of every related pairs found is shown in the report. - Now possible to change the title of the automatic report (using the --report-title option). - Better documentation.

Here is a description of the bugs that were fixed in the next release: - Fixes issue #4, where the automatic report failed if there were no duplicated markers in the dataset. - Fixes issue #5, where the automatic report failed if there were no duplicated samples in the dataset. - Fixes issue #6, where the scree plot is not included in the automatic report. - Fixes issue #10, where there was a problem when Unicode characters were present in figure paths. - Fixes issue #11, where the pipeline failed if ethnicity was checked without reference populations. - Fixes issue #12, where the wrong number of markers was included in the report. Now, only the number of unique markers is shown. - Fixes issue #13, where there was a problem with all paths when running the pipeline on Windows operating system. - Fixes issue #15, where the pyGenClean_merge_reports script fails when a directory contains a trailing slash ("/"). - Fixes a small bug, where there was an issue in the automatic report if only extract/exclude or keep/remove was used the in subset script. - Fixes a small bug, where output files with no data contained an empty line instead of being empty. - Fixes a small bug, where the script couldn't find a sample because it was sanitized for LaTeX.

- Python
Published by lemieuxl over 10 years ago

pygenclean - pyGenClean version 1.7.0

These changes will be included in the 1.7 version of pyGenClean: - automatic report - produce an automatic report (PDF using LaTeX) - script to merge multiple reports (for different steps of the QC pipeline) - summary files for a QC run including: - list of samples that were removed (with reason) - list of markers that were removed (with reason) - ethnicity module - possible to exclude the three reference panels when computing MDS values - bug fix when the three reference panels do not have the same list of markers - updated documentation

- Python
Published by lemieuxl over 10 years ago

pygenclean - pyGenClean version 1.6

- Python
Published by lemieuxl almost 11 years ago