3. Revision history

This page summarizes some of the more important changes between releases.

3.1. Current version

3.1.1. v2.3.0

Released: October 1, 2013

• General -ec performance improvements in bedops, bedmap and other applications.

• bedmap

  • Adds experimental support for --skip-unmapped option, which filters out reference elements which do not have mapped elements associated with them.

• starch

  • Fixed bug with starch where zero-byte BED input created a truncated and unusable archive. We now put in a “dummy” chromosome for zero-byte input, which unstarch can now unpack. This should simplify error handling with certain pipelines.

• unstarch

  • Can unpack zero-byte compressed starch archive (see above).
  • Changed unstarch --list option to print to stdout stream (previously sent to stderr).

• starch metadata library

  • Fixes array overflow bug with BEDOPS tools that take starch archives as inputs, which affected closest-features, bedops and bedmap.

• bam2bed and sam2bed conversion scripts

  • Rewritten bam2* and sam2* scripts from bash into Python (v2.7+).
  • Improved input validation against SAM v1 specification.
  • New --split option prints reads with ‘N’ CIGAR operations into separate BED elements.
  • New --all-reads option prints all reads mapped and unmapped.

• bedextract

  • Fixed stdin bug with bedextract.

• New documentation via readthedocs.org.

  • Documentation is now part of the BEDOPS distribution, instead of being a separate download.
  • We use readthedocs.org to host indexed and searchable HTML, PDF and eBook documents.
  • Documentation is refreshed and simplified, with a new installation/compilation guide.

• OS X compilation improvements

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

    This already makes compilation faster and easier, as well as reduces the size and complexity of Mac OS X builds and installer packages. When this process is complete, it will no longer be necessary to install GCC 4.7+ by way of MacPorts or other package managers, in order to build BEDOPS on OS X.

3.2. Previous versions

3.2.1. v2.2.0b

• Fixed bug with OS X installer’s post-installation scripts.

3.2.2. v2.2.0

Released: May 22, 2013

• Updated packages
  • Precompiled packages are now available for Linux (32- and 64-bit) and Mac OS X 10.6-10.8 (32- and 64-bit) hosts.
• Starch v2 test suite
  • We have added a test suite for the Starch archive toolkit with the source download. Test inputs include randomized BED data generated from chromosome and bounds data stored on UCSC servers as well as static FIMO search results. Tests put starch, unstarch and starchcat through various usage scenarios. Please refer to the Starch-specific Makefiles and the test target and subfolder’s README doc for more information.
• starchcat
  • Resolves bug with --gzip option, allowing updates of gzip -backed v1.2 and v1.5 archives to the v2 Starch format (either bzip2 - or gzip -backed).
• unstarch
  • Resolves bug with extraction of Starch archive made from BED files with four or more columns. A condition where the total length of additional columns exceeds a certain number of characters would result in extracted data in those columns being cut off. As an example, this could affect Starch archives made from the raw, uncut output of GTF- and GFF- conversion scripts.
• conversion scripts
  • We have partially reverted wig2bed, providing a Bash shell wrapper to the original C binary. This preserves consistency of command-line options across the conversion suite, while making use of the C binary to recover performance lost from the Python-based v2.1 revision of wig2bed (which at this time is no longer supported). (Thanks to Matt Maurano for reporting this issue.)

3.2.3. v2.1.1

Released: May 3, 2013

• bedmap
  • Major performance improvements made in v2.1.1, such that current bedmap now operates as fast or faster than the v1.2.5 version of bedmap!
• bedops
  • Resolves bug with --partition option.
• conversion scripts
  • All v2.1.0 Python-based scripts now include fix for SIGPIPE handling, such that use of head or other common UNIX utilities to process buffered standard output no longer yields IOError exceptions. (Thanks to Matt Maurano for reporting this bug.)
• 32-bit Linux binary support
  • Pre-built Linux binaries are now available for end users with 32-bit workstations.

Other issues fixed:

• Jansson tarball no longer includes already-compiled libraries that could potentially interfere with 32-bit builds.
• Minor changes to conversion script test suite to exit with useful error code on successful completion of test.

3.2.4. v2.1.0

Released: April 22, 2013

• bedops
  • New --partition operator efficiently generates disjoint segments made from genomic boundaries of all overlapping inputs.
• conversion scripts
  • All scripts now use sort-bed behind the scenes to output sorted BED output, ready for use with BEDOPS utilities. It is no longer necessary to pipe data to or otherwise post-process converted data with sort-bed.
  • New psl2bed conversion script, converting PSL-formatted UCSC BLAT output to BED.
  • New wig2bed conversion script written in Python.
  • New *2starch conversion scripts offered for all *2bed scripts, which output Starch v2 archives.
• closest-features
  • Replaced --shortest option name with --closest, for clarity. (Old scripts which use --shortest will continue to work with the deprecated option name for now. We advise editing pipelines, as needed.)
• starch
  • Improved error checking for interleaved records. This also makes use of *2starch conversion scripts with the --do-not-sort option safer.
• Improved Mac OS X support
  • New Mac OS X package installer makes installation of BEDOPS binaries and scripts very easy for OS X 10.6 - 10.8 hosts.
  • Installer resolves fatal library errors seen by some end users of older OS X BEDOPS releases.

3.2.5. v2.0.0b

Released: February 19, 2013

• Added Efficiently creating Starch-formatted archives with a cluster script variant which supports task distribution with GNU Parallel.
• Fixed minor problem with bam2bed and sam2bed conversion scripts.

3.2.6. v2.0.0a

Released: February 7, 2013

• bedmap
  • Takes in Starch-formatted archives as input, as well as raw BED (i.e., it is no longer required to extract a Starch archive to an intermediate, temporary file or named pipe before applying operations).
  • New --chrom operator jumps to and operates on information for specified chromosome only.
  • New --echo-map-id-uniq operator lists unique IDs from overlapping mapping elements.
  • New --max-element and --min-element operators return the highest or lowest scoring overlapping map element.
• bedops
  • Takes in Starch-formatted archives as input, as well as raw BED.
  • New --chrom operator jumps to and operates on information for specified chromosome only.
• closest-features
  • Takes in Starch-formatted archives as input, as well as raw BED.
  • New --chrom operator jumps to and operates on information for specified chromosome only.
• sort-bed and bbms
  • New --max-mem option to limit system memory on large BED inputs.
  • Incorporated bbms functionality into sort-bed with use of --max-mem operator.
• starch, starchcat and unstarch
  • New metadata enhancements to Starch-format archival and extraction, including: --note, --elements, --bases, --bases-uniq, --list-chromosomes, --archive-timestamp, --archive-type and --archive-version (see --help to starch, starchcat and unstarch binaries, or view the documentation for these applications for more detail).
  • Adds 20-35% performance boost to creating Starch archives with starch utility.
  • New documentation with technical overview of the Starch format specification.
• conversion scripts
  • New gtf2bed conversion script, converting GTF (v2.2) to BED.
• Scripts are now part of main download; it is no longer necessary to download the BEDOPS companion separately.

3.2.7. v1.2.5b

Released: January 14, 2013

• Adds support for Apple 32- and 64-bit Intel hardware running OS X 10.5 through 10.8.
• Adds README for companion download.
• Removes some obsolete code.

3.2.8. v1.2.5

Released: October 13, 2012

• Fixed unusual bug with unstarch, where an extra (and incorrect) line of BED data can potentially be extracted from an archive.
• Updated companion download with updated bam2bed and sam2bed conversion scripts to address 0-indexing error with previous revisions.

3.2.9. v1.2.3

Released: August 17, 2012

• Added --indicator option to bedmap.
• Assorted changes to conversion scripts and associated companion download.