• bugfix in taxify

Release notes

• general refactoring
• version number now printed in all output files

blobtools create

BAM parsing

• BAM parsing now fast(er)
• BAM is parsed with samtools view -F 4 -F 1028 -F 256 (only mapped, no optical-dupes, no 2nd-ary)
• Support for M/X/= in CIGAR string (previously only M's)

BAM/SAM/CAS parsing

• when parsing mapping files, blobtools automatically writes COV files

Taxonomy calculation

• if two highest scoring taxonomies for a given contig have EQUAL scores, taxonomy gets set to "unresolved"
• during plotting, the group "unresolved" gets treated as any other group
• new flag [--tax_collision_random] allows legacy behaviour (random selection of taxonomy)
• new argument [--min_diff FLOAT] sets minimal score difference between two highest scoring taxonomies of a contig in order for the contig to not be called "unresolved"

blobtools view

• refactored and is now fast(er)

supported views

• default view : table output, taxonomy columns are now numbered (1-based, for cut'ing). Can be turned off with [--notable]
• [--concoct]: outputs taxonomy and coverage information necessary to run concoct
• [--cov]: outputs coverage files (for using them in covplots)

blobtools map2cov

• previously bam2cov
• now supports BAM, SAM and CAS files (uses parsers in BtIO)
• implemented, so that one can convert multiple mapping files to lightweight COV format (i.e. using GNU parallel)

blobtools blobplot

Flags and arguments

• changed behaviour of [--multiplot]. Plots each group separately, then final plot of all groups.
• new flag [--cumulative]. Analogous to [--multiplot] behaviour in previous versions: incremental addition of groups
• new flag [--legend]. Plots legend in a separate figure, useful for slides.
• new argument [--lib LIBNAME]. Allows selecting particular covlib(s) to plot; lists available libraries when no argument is specified.
• new flag [--filelabel] : labels coverage axis based on coverage file
• fixed [--exclude], now removes group(s) from plotting and stats
• changed behaviour of [--colours FILE]. All groups not named in FILE are set to WHITE (for example see test_files/colours.txt)
• added example file for [--refcov FILE] (test_files/refcov.txt)

Scaling

• changed scaling of blobs in plots
• previously, blobs had an area of 65*(length/1,000) pixels^2. But if an assembly had a few very big contigs, these covered the smaller ones.
• now the scaling is done in the following way:
  • the biggest contig gets plotted as a blob of area 12,500 pixels^2
  • all other contigs get scaled proportionally
  • reference scale shows area of 5%, 10% and 25% length of longest contig

Misc

• added x-axis minor ticklabels, all ticklabels facing outwards
• fixed bug causing different plots to share filenames, causing overwriting

blobtools covplot

• same underlying library as blobplot.
• coverage axes are labelled based on coverage file
• axes can be relabelled using [--xlabel XLABEL] and [--ylabel YLABEL]
• maximal value for x/y-axes can be set using [--max FLOAT]

blobtools sumcov

• removed

blobtools taxify

• allows annotating similarity search results (from BLAST or Diamond) with TaxIDs using an ID-mapping-file, or a single TaxID

blobtools seqfilter

• allows filtering a FASTA file based on a list of headers

• Added support for parsing coverage from platanus headers

• added version number
• added license
• added prefix option for bam2cov
• added old function names again as aliases ("plot", "comparecov")

• new output format for bam2cov (now supports both base and read coverage)
• fixed bug in BtIO.readBam()

fixed bug regarding blobplot execution

Fixed bug in covplot (aka comparecov)

• Fixed bug in readcovplot