This is a log of updates I made. This should be short and I will not log changes in graphs and stats.

Todo

Need to add auto install in makefile for ivar
Need to fix infinite loop error in stich
- I have not been able to replicate this, but it has poped up in benchmarking.

oct 10, 2023

Adjusted default settings for alnSeq to prefer deletions over snps/matches. This should produce more accurate assemblies.

Switched to quast for measuring accuracy. This fixed an error that introduced extra snps.
- Ns, snps, and indels are now measured as per 1000 bases.
Added ivar support to buildcon
- I would suggest avoiding this.
Added medaka polishing of the consensus to the buildAmpCon.sh (calls buildcon) script
Modified runIvar.sh to take in primers. The benchmarking step is now using trimPrimers (00-programs) to trim primers when Ivar's internal trim is not being used.
Various modifications to benchAll.sh.

Fixed an infinite loop error in stich.
- This was due to unmapped amplicons being kept.
Added in an install option for ivar in the 00-programs make file
- use make MAKE_PROGRAM=make to complie with a differnt make program. This is here because the default make for the bsds is bsd make not gnu make (gmake).
- Also added in CPPFLAGS and LDFLAGS to the make file in 00-programs.

Fixed a couple errors in stich that caused crashes.
added ivar to the testing (00-scripts/runIvar.sh)
- ivar needs to be in 00-programs

Updated the benchAll.sh script to not run tests that have already been run. It will still subsample and mutate genomes that have been run, however, this is a small amount of the run time.
- For a restart You will have to clear everything, but the prefix-stats.tsv in 09.
- You will also have to move backup.xxx.reference.fasta to its correct directory (this is the unmutated reference).
Ended up with some mutated consensus in 06-schemes
- This was not a problem with the 07 directory (current graphed results).