Bugfix for min_nmut_read

What's new in v0.6.2

• Fixed bug with min_nmut_read not being accepted by main.run()

Full Changelog: v0.6.0...v0.6.2

Sliding correlations

What's new in v0.6.0

• Graph Pearson or Spearman correlations between two samples in sliding windows.
• Fix bug involving missing arguments in struct module.

Scatter Plots and Delta-Bar Plots

What's new in v0.5.0?

• Graph scatter plots and delta bar plots (i.e. the difference between two samples at each position) to visualize two mutational profiles over the same sequence.
  • Plots comparing two samples, as well as comparing different sources of data (e.g. masked vs. clustered) within one sample, are supported.
  • Plots involving two-sample comparisons are written to a sample directory named {sample1}__and__{sample2}.
  • Both ratios and counts are supported.
  • Stacked delta bar plots (breaking down differences between samples into each type of relation) are not supported.
• All graph types (except for stacked bar graphs) now support an option to normalize and winsorize ratiometric data (but not count-based data).
  • This feature is especially useful for delta bar plots comparing two samples with different levels of DMS/SHAPE treatment.
  • This feature works by specifying a quantile (--quantile / -q) in the range [0, 1] such that that quantile in the dataset is normalized to 1, all other data are scaled linearly, and any values greater than 1 (after scaling) are winsorized to 1.

Full Changelog: v0.4.1...v0.5.0

Informed Tables

What's new in v0.4.1

• The column "Informed" has been added to table files explicitly.
• Primarily, this addition was the simplest way to resolve a bug wherein running seismic graph seq -r n [TABLES ...] would crash because the "Informed" column was not present in the table.
• Additionally, this step should reduce any misconceptions that the "Covered" column is used as the denominator for e.g. mutation ratios.

Full Changelog: v0.4.0...v0.4.1

Sensible Alignment

What's new in v0.4.0

• In the steps that use a FASTA file of reference sequences, the file is now a required positional argument.
• In the align step, -x now means paired-end and -z now means single-end (and likewise for -X and -Z).
• A rudimentary user manual has been added.

Full Changelog: v0.3.0...v0.4.0

Input files as arguments

What's new in v0.3.0

• Files of input data (alignment maps, reports, tables, etc.) are now positional arguments instead of options. Thus, they can be given a) without a flag and b) using shell wildcard completion. The latter feature is more important, as it allows one to give arbitrary files that match a shell wildcard rather than specifying each file individually. For example, table out/report/sample3* instead of the much more verbose table -i out/report/sample31 -i out/report/sample32 -i out/report/sample33 -i out/report/sample34 -i out/report/sample35.
• The version attribute now exists, though a bug still causes its value to default to "unknown". Likewise, srna --version now produces output without crashing.

Why this is a minor release (v0.3.0) instead of a patch (v0.2.1)

The change in specifying input files on the command line interface causes a significant change in the command line interface for all steps except align. Since I increment patch numbers for smaller changes (e.g. minor bug fixes, internal optimizations) and minor version numbers for medium changes (e.g. affecting the user interface), this release fit better as a new minor version.

Full Changelog: v0.2.0...v0.3.0

Graph Positional Mutations in Clusters

What's new in v0.2.0

• Generate graphs from cluster tables using graph seq, in the same manner as for tables from the relate and mask steps. Multiple types of relationships can likewise be stacked with the --stack option, and the y-axis can be toggled between ratios and counts. The --arrange option controls whether one cluster is graphed per file, all clusters from one order are graphed per file, or all clusters from all orders are graphed in one file.
• In graphing, rename "fraction" to "ratio" (which is shorter, and the same length as "count") and rename the option from --yfrac to --y-count.
• Update the color palettes for graphs to be more aesthetically pleasing and more accessible for people with impaired color vision.
• Introduce the command line option --input-file (-i) to unify the separate command line options for alignment map (BAM) files (previously -b), report files (previously -r), and table files (previously -t). The aim is to eliminate confusion among these options and free up the -r and -t short options.
• Change the short versions of command line options, including sequence read (FASTQ) files (-s -> -x, -i -> -y, and -m -> -z, as well as the uppercase versions), the temporary directory (newly -t), and table/graph relationships (-c -> -r).
• Introduce a new logo for SEISMIC-RNA, as well as the source code that generates it (seismicrna/logo/logo.py).

Full Changelog: v0.1.3...v0.2.0

Deduplicate Accumulate

What's new in v0.1.3

• When version 0.1.2 enabled dropping duplicate read names, it inadvertently introduced a bug that caused subclasses of BitAccum to crash when checking for duplicate read names. This problem has been fixed.
• More detailed information on installation has been added to INSTALL.md and VENV.md.

Full Changelog: v0.1.2...v0.1.3

Handle Duplicate Read Names

What's new in v0.1.2

• The mask, cluster, and table steps now drop any read whose name matches the name of a previously-seen read. The first read given for each unique name is kept, and a warning message including the names of the dropped reads is issued. In earlier versions of the software, duplicate read names instead caused an error to be raised.

Update Alignment Defaults

What's new in v0.1.1

• The default mode of alignment has changed from end-to-end (which is still the default in Bowtie2 v2.5.1) to local. The lab decided on this change upon realizing that end-to-end mode can introduce large numbers of spurious mutations at the ends of reads prepared using random fragmentation and/or random priming, even following adapter trimming. Hence, we recommend end-to-end mode for and only for samples prepared as PCR amplicons with sequence-specific primers (for which local mode misses mutations within several bases of the ends of the amplicons). The end-to-end mode can still be enabled using the flag --bt2-end-to-end.
• The unit tests in the core subpackage have been split into one module of tests per module of code. Previously, they were all in the module core.test, which was becoming too large to develop. Unit tests of the other subpackages will likely be reorganized in the same manner in future versions.