Version 1.3.2

Fixes related to problems with samtools & bowtie2
-see issues #73, #72, #69, #68
-added new samtools and bowtie2 binaries which should work on more systems
-added checks for samtools and bowtie2 binaries; if binaries don't work instructions for replacing them are provided

Version 1.3.1

Changes to read alignment mode for snps and genes

• Switched back to global Bowtie2 read alignment in run_midas.py snps. This makes the program consistent with versions <= 1.2.2.
• run_midas.py genes module has always used local alignment, so there are no changes here
• Added option -m in run_midas.py to choose between global and local read alignment. For example, you can now runs the snps module using local alignment: run_midas.py snps /path/to/indir -1 /path/to/fastq -m local --aln_cov 0.75. This command will recapitulate the behavior of v1.3.0.
• Addresses issue #66

Version 1.3.0

Updated SNP calling

• Core-genome SNPs are determined based on pooling data across multiple samples
• SNPs are now reference-independent: the major and minor alleles are determined from aligned reads
• Added presets for commonly used sets of parameters: --core-snps, --core-sites, --all-snps, --all-sites
• Improved speed and parallelization
• Switched from global to local Bowtie2 read alignment; alignment coverage can be specified using the --aln_cov option

Updated DB building code

• Switched from USEARCH to VSEARCH
• Added function to write genome_info.txt file (issue #60 )

Updated binaries

• Bowtie2 (2.3.2) and Samtools (1.4) updated
• Allows for interleaved reads and improved parallelization

Updated documentation

• Added use cases for snp_diversity.py (issue #61 )

Bug fixes

• Fixed bug in run_midas.py snps (issue #57 )
• Test suite updated (issue #56 )
• Updated snp_diversity.py includeing bug fixes (issue #53 )

Version 1.2.2

Removed comment in code that caused mpileup to not run in snps.py

Version 1.2.1

Fixed bug in run_midas.py snps
-bug caused program to crash when parsing the mpileup output file

Version 1.2.0

Fixes bugs introduced in v1.1 and switches back to v1.0 strategy for estimating gene content.
Code and reference database should be stable going forward.

1. uses new database format
   -pan-genome genes defined at 99% identity threshold (same as v1.0)
   -includes mapping of genes to gene clusters at lower % identity thresholds (75,80,85,90,95)
   -enables sensitive read mapping while giving flexibility in defining pan genome gene families
   for other info, see: http://lighthouse.ucsf.edu/MIDAS/README.txt

2. updated build_midas_db.py
   -provides same features described in (1)

3. disabled map quality filtering in pan-genome pipeline (--mapq)
   -when genes are clustered at 99% identity, reads will often map to >1 gene, receive a low mapping quality, and get discarded
   -this feature was disabled to retain these reads

4. bug fixes
   -fixed estimation of marker gene coverage in 'run_midas.py species' (bug introduced in v1.1)
   -fixed normalization by marker gene coverage in 'run_midas.py genes'

5. 'run_midas.py genes' and 'merge_midas.py genes' report # of reads mapped to each gene cluster

Version 1.1.0

1. uses new database format
   species_ids now include the genus and species (ex: Bacteroides_vulgatus_57955)
   pan-genome genes now defined at 95% identity threshold
   removed 16S database for species profiling
   for other info, see: http://lighthouse.ucsf.edu/MIDAS/README.txt

2. run_midas.py and merge_midas.py require specification of database path
   enables users to specify their own database, or different versions of default database

3. improved run_midas.py snps
   -increased speed and decreased memory usage
   -fixed bug when computing depth at sites with N's
   -fixed bug when reference allele is not ATCG

4. added new scripts
   -build_midas_db.py
   allows users to build their own reference database
   -call_consensus.py
   calls consensus alleles at core-genomic sites
   enables construction of inter-sample phylogenetic trees
   -compare_genes.py
   quantify inter-sample differences in gene content
   -snp_diversity.py
   quantify intra and inter-sample population diversity

5. updated documentation

Publication release

v1.0

Fixed bug with bz2 files. Added check for file compression