v2.0.1

• bwa is again an option
• fixed samtools sort; updated samtools
• removed index case guessing
• removed tee from logging because you can't check the error codes
• New presets for mycobacterium
• New but unused script errorProneRegions.pl which detects regions that might be error prone, depending on your sequencing platform
• More documentation including those for visualization

v1.1.4g

An accumulation of random fixes has led to v1.1.4g. However the biggest factor in making a new release was the NCBI change from http to https, making the lambda dataset difficult to acquire without an updated release.

• edirect https fix embedded in make install 8798380
• xargs fix in a couple of scripts, replacing {} with $0 b90eae9
• C. bot presets now available
• set_diagnose checks for insert length sizes 6604151
• Array::IntSpan now installed with make install because it is a faster range class 82279e2
• Better version of makeRegions.pl, the script that will describe genomic regions, given a fasta, vcf, or bam file 09fb001
• Better version of the findPhages module 592c144
• Plugin for compatibility with Tinsel (for any plugin, you can run the plugin executable with the Lyve-SET project as a parameter) 47ee8cc
• Check for path to Java and to Grep, just in case those are not in the path e0d1573

v2.0

• More thought out VCF format
• Plugins starting with Tinsel
• Better phage finding
• Array::IntSpan for faster range calculations
• C. bot settings
• Various bug fixes
• smarter makeRegions.pl
• avoiding mergeVcf namespace issue with snp-pipeline
• Samtools and Bcftools v1.3.1

v1.1.4f

• Fixed bug in matrixToAlignment where a dot was incorrectly interpreted as REF instead of N.
• Removed ridiculous output files that were polluting the main project directory
• Making a symlink tree.dnd that points to out.RAxML_bipartitions
• Creating a DOI from this release

v1.1.4e

• Fixed filterMatrix bug where sometimes invariant sites could appear
• Fixed shuffleSplitReads bug where shuffling from a different directory could cause the script to crash

v1.1.4d

• Fixed allowedFlanking bug. filterMatrix is much more straightforward and is reflected in its usages
• Fixed other scripts that call filterMatrix

v1.3.1 - Just for testing purposes

corrected values for default DP4

Still under testing...

v1.1.8d

v1.1.8d

v1.1.8c

Version 1.1.8c

v1.1.6b

Version 1.1.6b