BEDOPS 2.4.3 released

[AlexReynolds]

BEDOPS 2.4.3 release (GitHub)

Compilation improvements

• Shane Neph put in a great deal of work to enable parallel builds (e.g., make -j N to build various targets in parallel). Depending on the end user’s environment, this can speed up compilation time by a factor of 2, 4 or more.
• Fixed numerous compilation warnings of debug builds of starch toolkit under RHEL6/GCC and OS X 10.10.1/LLVM.

New bedops features

• Added --chop and --stagger options to “melt” inputs into contiguous or staggered disjoint regions of equivalent size.
• For less confusion, arguments for --element-of, --chop and other bedops operations that take numerical modifiers no longer require a leading hyphen character. For instance, --element-of 1 is now equivalent to the former usage of --element-of -1.

New bedmap features

• The --sweep-all option reads through the entire map file without early termination and can help deal with SIGPIPE errors. It adds to execution time, but the penalty is not as severe as with the use of --ec. Using --ec alone will enable error checking, but will now no longer read through the entire map file. The --ec option can be used in conjunction with --sweep-all, with the associated time penalties. (Another method for dealing with this issue is to override how SIGPIPE errors are caught by the interpreter (bash, Python, etc.) and retrapping them or ignoring them. However, it may not a good idea to do this as other situations may arise in production pipelines where it is ideal to trap and handle all I/O errors in a default manner.)
• New --echo-ref-size and --echo-ref-name operations report genomic length of reference element, and rename the reference element in chrom:start-end format (useful for labeling rows for input for matrix2png or R or other applications).

bedextract

• Fixed upper-bound bug that would cause incorrect output in some cases

Conversion scripts

• Brand new C99 binary called convert2bed, which wrapper scripts (bam2bed, etc.) now call. No more Python version dependencies, and the C-based rewrite offers massive performance improvements over old Python-based scripts (about 1.5-8x faster than some alternatives).
• Added parallel bam2starch script, which parallelizes creation of Starch archive from very large BAM files in SGE environments.
• Added bug fix for missing code in starchcluster.gnu_parallel script, where the final collation step was missing.
• The vcf2bed script now accepts the --do-not-split option, which prints one BED element for all alternate alleles.

Starch archival format and compression/extraction tools

• Added duplicate- and nested-element flags in v2.1 of Starch metadata, which denote if a chromosome contains one or more duplicate and/or nested elements. BED files compressed with starch v2.5 or greater, or Starch archives updated with starchcat v2.5 or greater will include these values in the archive metadata.
• The unstarch extraction tool offers --has-duplicate and --has-nested options to retrieve these flag values for a specified chromosome (or for all chromosomes).
• Added --is-starch option to unstarch to test if specified input file is a Starch v1 or v2 archive.
• Added bug fix for compressing BED files with starch, where the archive would not include the last element of the BED input, if the BED input lacked a trailing newline. The compression tools now include a routine for capturing the last line, if there is no newline.

Documentation improvements

• Remade some image assets throughout the documents to support Retina-grade displays
• Updated Homebrew (homebrew-science) package installation instructions