Tool:Bedops V2.4 Released

Question

[Alex Reynolds]

BEDOPS is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It is fast and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data. More information is described in our Overview document, with specifics for each component on our main documentation site.

We have released BEDOPS v2.4. This revision includes several new features, performance enhancements and fixes:

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• bedmap
  • Added new --echo-map-size and --echo-overlap-size options to calculate sizes of mapped elements and overlaps between mapped and reference elements.
  • Improved performance for all --echo-map-* operations.
  • Improved documentation.

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• Major scalability enhancements and fixes to sort-bed
  • Improved performance.
  • Fixed memory leak.
  • Added support for millions of distinct chromosomes.
  • Improved internal estimation of memory usage with --max-mem option.

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• Added support for compilation on Cygwin (64-bit). Refer to the installation documentation for build instructions.

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• starchcat
  • Fixed embarassing buffer overflow condition that caused segmentation faults on Ubuntu 13 hosts.

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• Major scalability enhancements and features in *2bed and *2starch conversion scripts
  • Formerly v2.3 Python-based scripts no longer use temporary files and now stream data internally, which reduces file-based I/O and greatly improves performance, getting close to speeds found in simpler v2.2 and previous-versioned scripts. This change also reduces the need for large amounts of free space in a user’s /tmp folder, particularly relevant for users converting multi-GB BAM files.
  • Improved error handling, locating starch, sort-bed, wig2bed_bin and samtools in the user's environment and quitting with the appropriate error state if the dependencies cannot be found.
  • Improved documentation. In particular, we have added lookup tables to each script’s documentation page which describe how columns map from original data input to BED output.
  • bam2bed/starch and sam2bed/starch now offer a --custom-tags <value> option to support a comma-separated list of custom tags (cf. Biostars discussion).
  • vcf2bed/starch now offers --snvs, --deletions and --insertions options to segregate variants by category.
  • bam2bed, sam2bed, gff2bed, psl2bed, vcf2bed and wig2bed (as well as *2starch equivalents) now offer a --keep-header option to preserve metadata and header sections as BED elements. Metadata records are kept in a pseudo-chromosome called _header. By using the --keep-header option, conversion of those formats is completely non-lossy.

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• Added provisional OS X uninstaller project to allow end user to more easily remove older versions of BEDOPS tools.

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• Cleaned up various compilation warnings found with clang/clang++ and GCC kits.

Answer 1

[Alex Reynolds]

Today, we released BEDOPS v2.4.1. This adds the following new features and fixes:

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• bedmap
  • Added --fraction-both and --exact (--fraction-both 1) to the list of compatible overlap options with --faster.
  • Added 5% performance improvement with bedmap operations without --faster.
  • Fixed scenario that can yield incorrect results.

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• sort-bed

  • Added --tmpdir option to allow specification of an alternative temporary directory, when used in conjunction with --max-mem option.

    This is useful if the host operating system’s standard temporary directory (e.g., /tmp on Linux or OS X) does not have sufficient space to hold intermediate results.

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• Improvements to *2bed / *2starch conversion scripts
  • Improvements to error handling in Python-based conversion scripts, in the case where no input is specified.
  • Fixed typos in gff2bed and psl2bed documentation.

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• OS X compilation improvements

  • We have completed changes to the OS X build process for the remaining half of the BEDOPS binaries, which now allows direct, full compilation with Clang/LLVM (part of the Apple Xcode distribution).

    All OS X BEDOPS binaries now use Apple’s system-level C++ library, instead of GNU’s libstdc++. It is no longer required (or recommended) to use GNU gcc to compile BEDOPS on OS X.

    Compilation is faster and simpler, and we can reduce the size and complexity of Mac OS X builds and installer packages. By using Apple’s C++ library, we also eliminate the likelihood of missing library errors.

    In the longer term, this gets us closer to moving BEDOPS to using the CMake build system, to further abstract and simplify the build process.

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• Cleaned up various compilation warnings found with clang / clang++ and GCC kits.