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A regression test suite and historical results for the Canu single molecule sequence assembler.

Background

This is a set of scripts and configurations to compare results of Canu across different code points. The driver script will update a local copy of the canu github repo, checkout a specific version of Canu, and launch a (user-supplied) set of assemblies.

Each assembly will compare itself against a reference genome (using quast) and then compare quast results against a previously chosen curated assembly and report differences in the quast results.

Usage

The main driver is regression.pl. This will update the local repo, checkout a specific version of Canu, build, and then launch assemblies on the grid.

The "chosen curated assembly" can be updated using update-refasm.sh.

Milestones

Nothing more than a list of special dates. It's quite out of date.

Date Hash Milestone
2020-10-16-1821 5638f7d9a5379373310ab62c28aa0cdbd864722d Canu 2.1.1, branch v2.1-maintenance
2020-09-18-1243 b9826425676a2eb019fd2ad2f240f2eebd79c35a mhap -minlength option
2020-08-24-1052 dd71f16d5c31e0f6d30297c215a9c62353079da9 Canu 2.1, branch v2.1-maintenance
2020-08-19-2326 7bb8a2435e3f8d2d9a73be44b2c9fef3cccd32a5 Canu 2.1 master, (just after release)
2020-07-22-1735 afcb34fde3fb9445d57f8b311f92794f9c96baa5 Build in 'build' instead of 'OSTYPE-MACHINETYPE'. (Regression might not work before this)
2020-03-18-0351 541200a23245ebe71ad2b46f6d8f500431a1725e Canu 2.0, branch v2.0-maintenance
--------------- ---------------------------------------- ------------------------------------------------------
--------------- ---------------------------------------- ------------------------------------------------------
2018-09-18-0752 trio support full run
2018-09-05-1307 meryl v2 full run (complete)
2018-08-13-0800
2018-07-30-1450
2018-07-26-1654
2018-05-16-1124
2018-05-08-1454 edlib patches
2018-05-04-0314 last seqStore change
RED fails, ran by hand (fixed on 05-05)
2018-04-16-0545 bogart bugs, after ovlStore bugs fixed
FAILED - gkpStore partitioning (still) has bad BLOB pointers
2018-03-28-1108 before ovlStore changes
FAILED - gkpStore partitioning has bad BLOB pointers
2018-03-13-2009 gkpStore changes
FAILED - gkpStore partitioning has bad BLOB pointers
2018-03-13-1715 before gkpStore changes
2018-02-27-0846 v1.7
--------------- ---------------------------------------- ------------------------------------------------------
2018-02-09-1146 Use both read length and overlap length to filter evidence for correction.
No change and I forget (in the two months it took to run it) what was exactly being tested.
NOTE! These have BAD job sizes for RED, resulting in VERY VERY small jobs.
2018-02-08-1804 (before the next one)
--------------- ---------------------------------------- ------------------------------------------------------
2017-08-14-1539 v1.6
2017-10-11-1435 Minor bugfixes, new installation structure,
2017-10-05-2341 One gkpStore.
Pseudo-QV's for corrected reads.
Output read names from mhap, not just per-job ID.
Remove -w option from overlapInCore.
2017-09-23-1710 Bug fix; don't crash when no corrected sequence is generated for any read.
2017-09-22-1613 Emit only single longest corrected read piece. Bug fixes in grid support.
2017-09-20-1513 Bug fixes in overlap store histogram.
2017-09-18-1358 Use corStore for correction.
Estimate overlap scores; changes to overlap store stats data.
Overlap scores are 16-bit integers.
Fix inconsistent overlap scores introduced in last commit.
2017-08-24-0051 KNOWN BAD; overlap scores computed using inconsistent functions!
Merge falcon_sense and input generation.
2017-08-14-1539 v1.6 (MISSING); just minor stuff since last commit.
2017-08-11-0829 Minor logging change and bug fix.
2017-08-10-1830 Bogart: dead bubble popping code removal, errorProfile memory optimization.
2017-08-02-0645 Bug fixes.
2017-07-28-2128 Bug fixes and intermediate file cleanup.
2017-07-25-2009
2017-07-03-1413
2017-06-29-1114
2017-06-09-1607
2017-06-07-1055
2017-05-19-1828
2017-05-10-1930
--------------- ---------------------------------------- ------------------------------------------------------
2017-04-17-1531 v1.5
2017-03-10-0053 alignPair rewrite
2017-03-10-0051 alignPair rewrite, previous commit
2017-01-27-0903 errorRate replacement
2017-01-27-0803 errorRate replacement, previous commit
2017-01-06-0241 stageDirectory (so nothing big will run before this)
--------------- ---------------------------------------- ------------------------------------------------------
2016-12-12-2155 v1.4
2016-11-08-1117 first that works
2016-11-07-1826 adds support for onSuccess, but doesn't work
--------------- ---------------------------------------- ------------------------------------------------------

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Regression test cases and results for Canu.

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