JaneliaSciComp/msg

Issues

• get_sample_data.sh file locations have changed

  #44 opened 3 years ago by pmcarlton
  0

• Add support for paired-end read alignment

  #47 opened 3 years ago by fdchevalier
  1

• MSG can't process paired-end sequences

  #46 opened 3 years ago by fdchevalier
  0

• add msg.cfg parameter for one.sit.per.read in fit-hmm.R

  #41 opened 11 years ago by gregpinero
  0

• Have MSG Log all version numbers of dependencies

  #39 opened 12 years ago by gregpinero
  0

• summaryPlots.R - Single Individual Fix

  #38 opened 12 years ago by gregpinero
  0

• Parsing config files - skip over blank values

  #37 opened 12 years ago by gregpinero
  0

• / Character in FASTA sequence identifiers causes MSG to think references are directories

  #36 opened 12 years ago by gregpinero
  2

• Parse gzipped fastq files directly

  #20 opened 12 years ago by gregpinero
  0

• Add verbosity option for data output

  #16 opened 12 years ago by gregpinero
  1

• summaryPlots.R - Generate Off-diagonal LOD on Thinned Data instead of full data

  #34 opened 12 years ago by gregpinero
  0

• MSG incorrectly skips generating stampy index files for indiv's on some reruns

  #33 opened 12 years ago by gregpinero
  0

• Handle slashes (and other chars) in barcodes

  #32 opened 12 years ago by gregpinero
  0

• Parsing - If an individual has no reads, produce error message and continue instead of dying.

  #31 opened 13 years ago by gregpinero
  1

• summaryPlots.R - On memory error in thinning - should show helpful message

  #30 opened 13 years ago by gregpinero
  0

• Update Code with Tina's changes

  #17 opened 13 years ago
  0

• Don't quality trim files if a trimmed file is already present

  #29 opened 13 years ago by gregpinero
  0

• Remove poor quality reads from fastq file right away using TQSfastq.py

  #26 opened 13 years ago by gregpinero
  3

• feature: msgRun1.sh doesn't need to wait can be in parallel

  #6 opened 13 years ago
  2

• Make code run faster

  #15 opened 13 years ago by gregpinero
  0

• msg.pl - updating genomes step - samtools view command references missing var

  #21 opened 13 years ago by gregpinero
  1

• Create a new tag, and figure out best way to include release/tag # in MSG

  #24 opened 13 years ago by gregpinero
  0

• Fix Stampy Issue: stampy: Error: invalid data stream - and remove ln -s workaround

  #28 opened 13 years ago by gregpinero
  0

• Create more documentation - see notes

  #27 opened 13 years ago by gregpinero
  0

• Include More Dependencies in Source/GitHub

  #23 opened 13 years ago by gregpinero
  0

• extract ref alleles - dynamically set low memory mode based on input file size and avail. memory

  #19 opened 13 years ago by gregpinero
  1

• Change Perl Modules to use strict mode

  #22 opened 13 years ago by gregpinero
  0

• If extract_ref_alleles finds no references, it should die w/ useful error, con't pipeline w/ orig. genome

  #18 opened 13 years ago by gregpinero
  0

• Github - Set up release tags

  #10 opened 13 years ago by gregpinero
  0

• Feature: Clean up un-needed intermediate data files after run

  #4 opened 13 years ago
  0

• Feature: change code to use max_coverage

  #7 opened 13 years ago
  0

• Investigate (and possibly fix) source of stochasticity

  #11 opened 13 years ago by gregpinero
  0

• Bug: Don't require blank line on last line of barcodes file

  #3 opened 13 years ago
  2

• min_coverage parameter is not read from msg.cfg

  #9 opened 13 years ago by gregpinero
  0

• Validate that all output files were created

  #13 opened 13 years ago by gregpinero
  0

• Bug: allow spaces around = in msg.cfg

  #2 opened 13 years ago
  0

• Investigate and Fix Strange Error Message

  #14 opened 13 years ago by gregpinero
  0

• fit-hmm.R make maximum number of reads a parameter passed in from msg.cfg

  #12 opened 13 years ago by gregpinero
  0

• Bring in pull requests from tinathu/msg

  #1 opened 13 years ago
  1

• Other MSG repos: Take down, or put up note that this is master repo

  #8 opened 13 years ago
  0

• Change email for login for JanaliaSciComp user to something generic for Janelia

  #5 opened 13 years ago
  0