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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

  • main workflow figure for ALSO.
  • readthedocs.

[0.9.8] - 2022-10-13

changed

[0.9.4] - 2022-06-25

added

  • Developed Python implementation for filtering bam files by txt-file lists of QNAMEs
  • Rewrote/refactored code to handle input for Python-implemented filtering

[0.9.3] - 2022-06-15

fixed

  • Update README.md and log.md files

[Unreleased]

  • #TODO Troubleshoot max memory for JVM when running picard FilterSamReads
  • #TODO Consolidate shell, R functions into one script for each language
  • #TODO Remove harcoded path to GS installation of picard from scripts #DONE

[0.9.2] - 2022-06-04

  • Pipeline is completed; passed local unit tests with small files; can call it with driver_allelic-segregation.sh
  • Adding instructions for using driver_allelic-segregation.sh to README.

[Unreleased]

  • #TODO Test on the GS HPC with large files: Do we need to increase max heap memory to the JVM when running picard?
  • #TODO Clean up messages output by the driver
  • #TODO Determine and list all dependencies

[0.9.1] - 2022-05-23

  • Addressing error in preprocessing pipeline in which some duplicate QNAMEs persist in processed bam.
  • Adding instructions for using the correction script, 03-remove-duplicate-qnames.sh.
  • #TODO Add corrections in 03-remove-duplicate-qnames.sh to the initial preprocessing script: 03-filter-problematic-qnames-HPC.sh #DONE

[0.8.9] - 2022-05-11

fixed

[Unreleased]

  • Will create a pull request to move 03-remove-duplicate-qnames.sh from the ALSO repo to the Shendure-Lab sciatac pipeline repo after the allele score comparison module is completed
  • Kris will work on the allele score comparison module

[0.8.8] - 2022-05-10

added

  • Kris' new version preprocess module passed tests from both Kris and Gang
  • Gang runs the preprocess module on all samples

[0.8.8] - 2022-05-04

added

  • Gang tested on the one sample from mm10, one sample from CAST
  • Kris tested on the largest bam that we have

fixed

  • Bill cleaned up the space of vol6; all future results will be stored in vol6
  • Update the workflow according to Kris's newest preprocess module (4 steps)

[0.8.7] - 2022-05-02

added

  • Add worflow script 03-filter-qname.sh, an in-progress shell pipeline to handle the preprocessing
  • Write code for handling intermediate files, e.g., deleting, keeping, etc.

fixed

  • Upload/update test code for debugging the preprocess module
  • Update README for using the script
  • Further updates, cleanup of the README

[0.7.9] - 2022-04-13

fixed

  • Upload/update test code for debugging the preprocess module
  • Update README for information on running the test code

[0.7.8] - 2022-04-08

fixed

  • Replace the workflow chart
  • Upload code to debug preprocess module

[0.7.7] - 2022-03-27

added

  • For 04, add additional code to remove singletons from split bam files

[0.7.6] - 2022-03-26

added

  • Add additional options, corrections to 04-split-index-repair-bam.sh
    • "mm10" mode, which does not output POS and MPOS bed files
    • "strain" mode, which outputs POS and MPOS bed files
    • Additional to sort and index bam infile if necessary
  • Update associated test script for new modes

[0.7.4] - 2022-03-24

fixed

  • Update workflow chart with yellow box (preprocess step)

added

  • Update run script for preprocess step

[0.7.3] - 2022-03-23

added

  • Add 06-convert-bam-to-df_join-bed_write-rds.R

[0.7.2] - 2022-03-24

removed

  • Clean up repo, removing unneeded scripts and data files

fixed

  • Update dependencies listed in README

[0.7.1] - 2022-03-20

added

  • Add 05-lift-strain-to-mm10.sh
  • Add script to download and process liftOver chain files: get-liftOver-chains.sh
  • Add script to downsample bam files: generate-downsampled-bam.sh
  • Minor changes to workflow scripts 01 and 04
  • Update README, including sample-call section

[0.7.0] - 2022-03-19

fixed

  • Update workflow image
  • Update README for (filter reads with MAPQ < 30; then removing singleton; subread repair)
  • Update code for (filter reads with MAPQ < 30; then removing singleton; subread repair.)

[0.5.0] - 2022-03-17

added

  • Add new workflow image

fixed

  • CX updated get_unique_fragments.py. Kris will test it on duplicates
  • After Shendure lab pipeline, we will first filter reads with MAPQ < 30; then removing singleton; (Kris: no need to sort anymore) subread repair