Author Topic: BEDOPS v2.4 released  (Read 4849 times)

AlexReynolds

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BEDOPS v2.4 released
« on: January 09, 2014, 02:29:23 PM »
We have released BEDOPS v2.4 (https://github.com/bedops/bedops/releases/tag/v2.4.0). This revision includes several new features, performance enhancements and fixes:

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.

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.

Added support for compilation on Cygwin (64-bit)


starchcat

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

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 userís /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 scriptís 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 at http://www.biostars.org/p/87062/).
  • 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.

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

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