[2.0.3] - 2019-07-01

Changed

• Optimized UMI de-duplication step.

Fixed

• Fraction of final output VS input with prefix.

[2.0.2] - 2018-04-04

Changed

• Updated submodules.

Fixed

• Now properly summarizing preseq reports with multiqc.
• Fixed alignment fraction calculation.

[2.0.1] - 2018-01-16

Fixed

• Fixed secondary alignments removal during SAM filtering step.
• Fixed chromosome removal during SAM filtering step.

Added

• multiqc report recap as a last step of the pipeline.
• Version tag to log.

[2.0.0] - 2017-01-09

Added

• preseq package as a git submodule.
• Library complexity estimation step, using preseq package.
• Version tracking to bed header and summary tables.

Changed

• Clarified neatness level labeling.
• Promoted centrality estimate from dev to tool.
• Now using samtools and awk for SAM file filtering.
• Updated documentation.

Removed

• Useless thread declaration when running FASTQC tool.
• Binning and plotting step, stored in deprec folder.

Fixed

• Input option exceptions.

[1.1.0] - 2017-07-26

Added

• Neatness level for automatic clean-up of intermediate files.
• Multi-library analysis.
• Saving orphan reads in orphan.txt.

Changed

• Cutsite sequence option, moved to single option from pattern file.
• pat_files to patterns.tsv (renamed).
• Log, now divided by library.

Fixed

• Bug in SAM filter that crashed the script if no chromosome is removed.

Removed

• Sub-step queries for filepaths.

[1.0.1] - 2017-07-17

Added

• Debug mode to global centrality script.
• Optional intermediate ranking to global centrality script.
• Counting UMI duplicates during strict deduplication step.

Changed

• Read quality filter, optimized memory usage.
• Summary update method to avoid creationg of broken lines.

Fixed

• Global centrality option.
• Bed file creation: multiple pipeline run would append new bed files to old ones.

[1.0.0] - 2017-03-29

Added

• Input parameter support with getopt in main.
• Auxillary intermediate data aux subfolder.
• Counts of reads filtered from SAM in the summary.
• Command line saved in aux/CMD file.
• X/Y chromosomes filter during SAM filter step.
• MAPQ level in SAM filter output.
• SAM filter step log.
• UMI preparation step log.
• Header line to bed file.
• Global centrality script.
• Cumulative of ratio and ratio of cumulative approaches to global centrality script.
• Properly formatted bed files per condition.

Changed

• File location, moved code to bin subfolder.
• Output structure, moved conditions into conditions subfolder.
• Output structure, moved output plots into plots subfolder.
• Read trimming script, optimized.
• Main script, now using modules.
• File structure, moved scripts to separate folder.
• Pos2cutsite script, optimized by calculating distance only from the 2 closest cutsite.
• Bed creation, moved to separate script.
• Barcode sequence option, moved to pat_files.

Fixed

• Read trimming.
• rmX/rmY option report.

[0.1.0] - 2017-03-13

First release.