Issues

• Ref sequence output for sequencer.py is a concatenation of the mut and wt

  bugsize: S
  summerela/ShortStack#234 · Filter by author NicoleEO opened on Jun 26, 2019

• Re-write pipeline to align against WT and all variants then select best alignment.

  summerela/ShortStack#230 · Filter by author summerela opened on Apr 18, 2019

• standardize panel-generated inputs for hexsembler

  size: S
  summerela/ShortStack#224 · Filter by author kzeller2 opened on Mar 7, 2019

• Test Nsolver Output

  size: S
  summerela/ShortStack#220 · Filter by author kzeller2 opened on Mar 7, 2019
  1

• validator for standard outputs

  size: S
  summerela/ShortStack#218 · Filter by author kzeller2 opened on Mar 7, 2019

• FTM output to Nsolver-compatible inputs

  size: S
  summerela/ShortStack#216 · Filter by author kzeller2 opened on Mar 7, 2019

• Define release and test cycle

  epic: implement qa proceduressize: S
  summerela/ShortStack#213 · Filter by author kzeller2 opened on Mar 7, 2019
  1

• update FTM documentation (SDD template)

  epic: implement regular updates of documentationsize: S
  summerela/ShortStack#200 · Filter by author kzeller2 opened on Mar 7, 2019

• Add handling of reverse compliment

  enhancementpri: Msize: M
  summerela/ShortStack#185 · Filter by author summerela opened on Feb 15, 2019 · Program Increment 1
  

• Add information differentiating unique WT hexamers to bc_counts/all_counts/rawCounts

  summerela/ShortStack#182 · Filter by author joephun opened on Feb 7, 2019 · Program Increment 1

• Output IUPAC rather than N for sites with ambiguous sites (more than 1 call)

  summerela/ShortStack#155 · Filter by author Vera-D opened on Jan 10, 2019 · Program Increment 1

• Optimize sequence.py

  summerela/ShortStack#135 · Filter by author summerela opened on Jan 3, 2019 · Program Increment 1

• Rewrite ShortStack to only convert color to nucleotides after calculating hamming distance on bit arrays.

  enhancementpri: Lsize: M
  summerela/ShortStack#130 · Filter by author summerela opened on Dec 27, 2018 · Program Increment 1

• Add arrival/survival plots to ShortStack

  enhancementpri: Lsize: M
  summerela/ShortStack#125 · Filter by author summerela opened on Dec 19, 2018 · Program Increment 1

• Add coverage plots to ShortStack

  enhancementpri: Lsize: M
  summerela/ShortStack#124 · Filter by author summerela opened on Dec 19, 2018 · Program Increment 1

• Add time course plot to ShortStack

  enhancementpri: Msize: L
  summerela/ShortStack#123 · Filter by author summerela opened on Dec 19, 2018 · Program Increment 1
  1

• Adding run time and performance output to short stack run_info

  summerela/ShortStack#120 · Filter by author Vera-D opened on Dec 18, 2018 · Program Increment 1

• Compile as python package to pip install

  pri: Mrequirementsize: M
  summerela/ShortStack#119 · Filter by author kzeller2 opened on Dec 17, 2018 · Program Increment 1
  4

• Add P(val) placeholder function

  size: S
  summerela/ShortStack#116 · Filter by author kzeller2 opened on Dec 13, 2018 · Program Increment 1
  

• Run ShortStack on AWS

  pri: Lsize: M
  summerela/ShortStack#99 · Filter by author Vera-D opened on Dec 4, 2018 · Program Increment 1
  

• Add survival_percent equivalent to Shortstack configuration

  size: M
  summerela/ShortStack#77 · Filter by author kzeller2 opened on Nov 28, 2018 · Program Increment 1

• Capture Error Modes

  summerela/ShortStack#75 · Filter by author summerela opened on Nov 27, 2018 · Program Increment 1
  2

• Single molecule run testing - Does increasing the number of targets fed decrease accuracy of matching to NRAS.1 - Feed different amounts of target seqs as fasta

  pri: Lsize: S
  summerela/ShortStack#49 · Filter by author kzeller2 opened on Oct 29, 2018 · Program Increment 1

• Software - Secondary Sequencing Analysis - Determine output files of this panel

  pri: Msize: L
  summerela/ShortStack#48 · Filter by author kzeller2 opened on Oct 29, 2018 · Program Increment 1

• Software - Secondary Sequencing Analysis - Software can generate required files

  pri: Msize: L
  summerela/ShortStack#47 · Filter by author kzeller2 opened on Oct 29, 2018 · Program Increment 1