v0.7.5: Version 0.7.5

Version 0.7.5

Global speedups, friendlier error handling and miscellaneous bug fixes.
Documentation updates (thanks @kyleabeauchamp; #67).
Expanded unit tests & restored continuous integration (TravisCI).
Raised the minimum pandas version to 0.17.1, the latest.

rescale (new command; #64):

• Adjust .cnr or .cns files for normal contamination or subclone fraction.
• Re-center log2 values by median (the usual), mode, mean, or biweight location.

segment:

• Detect outlier bins and ignore them during segmentation using a method similar to BIC-seq. Command line option: --drop-outliers; any outlier bins found will be logged.

coverage:

• If the given target BED files is missing the 4th column (gene names), fill in the dummy name "-" instead of crashing.

segmetrics:

• Expose alpha and number of bootstraps as command-line options -a/--alpha and -b/--bootstrap for calculating confidence intervals.

antitarget:

• Reduce default bin size from 150kb to 100kb.

fix:

• Speed improvements: now about 20 times faster on exomes.

API changes:

• Gene names to treat as meaningless and to ignore in reporting (by default "-", ".", "CGH") can be globally configured in cnvlib/params.py (params.IGNORE_GENE_NAMES).
• vary.VariantArray (used in scatter) can now parse VCF files with no samples (genotypes) as a table of plain loci.