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@arq5x arq5x released this Dec 17, 2019 · 47 commits to master since this release

  1. Fixed a bug (#803) that mistakenly removed a BAM/CRAM header line (sorting criteria).
Assets 4

@arq5x arq5x released this Dec 9, 2019 · 53 commits to master since this release

  • Fixed a bug that now allows blocked intersection to be counted based on unique base pairs of overlap. The resolution for issue 750 in version 2.29.0 mistakenly allowed for fractional overlap to be counted based upon redundant overlap.
  • Moved to Github Continuous Integration for automatic testing.
  • Fixed a bug that injected erroneous quality values with BAM records had no valid quality values.
  • Fixed a bug that destroyed backwards compatibility in the getfasta tool. Thanks to Torsten Seeman for reporting this.
  • Fixed a corner case bug in the reldist tool.
  • Fixed a bug in the bedtobam tool that caused the last character in read names to be removed.
  • Fixed a bug causing a segfault in the jaccard tool.
  • Fixed a bug causing a corner case issue in the way coordinates are reported in the flank tool.
Assets 3

@arq5x arq5x released this Sep 3, 2019 · 89 commits to master since this release

  1. Added a new -C option to the intersect tool that separately reports the count of intersections observed for each database (-b) file given. Formerly, the -c option reported to sum of all intersections observed across all database files.
  2. Fixed an important bug in intersect that prevented some split reads from being counted properly with using the -split option with the -f option.
  3. Fixed a bug in shuffle such that shuffled regions should have the same strand as the chose -incl region.
  4. Added a new -L option to Limit the output of the `complement tool to solely the chromosomes that are represented in the -i file.
  5. Fixed a regression in the multicov tool introduced in 2.28 that caused incorrect counts.
  6. Added support for multi-mapping reads in the bamtofastq tool.
  7. Fixed a bug that prevented the “window” tool from properly adding interval “slop” to BAM records.
  8. Fixed a bug that caused the slop tool to not truncate an interval’s end coordinate when it overlapped the end of a chromosome.
  9. Added support for the “=” and “X” CIGAR operations to bamtobed.
  10. Various other minor bug fixes and improvements to documentation.
Assets 3

@arq5x arq5x released this Mar 23, 2019 · 160 commits to master since this release

  1. Included support for htslib to enable CRAM support and long-term stability (Thanks to Hao Hou!)
  2. Included support for genomes with large chromosomes by moving to 64-bit integers throughout the code base. Thanks to Brent Pedersen and John Marshall!
  3. We now provide a statically-linked binary for LINUX (not OSX) systems (see "bedtools" link below).
  4. As a result of 1-3, tools are ~10% faster.
  5. Various minor bug fixes.
Assets 4

@arq5x arq5x released this Dec 14, 2017 · 287 commits to master since this release

Fixed a bug in the Makefile that caused a substantial penalty in performance.

Assets 3

@arq5x arq5x released this Dec 6, 2017 · 293 commits to master since this release

Version 2.27.0 (6-Dec-2017)

  1. Fixed a big memory leak and algorithmic flaw in the split option. Thanks to Neil Kindlon!
  2. Resolved compilation errors on OSX High Sierra. Many thanks to @jonchang!
  3. Fixed a bug in the shift tool that caused some intervals to exceed the end of the chromosome. Thanks to @wlholtz
  4. Fixed major bug in groupby that prevented proper functionality.
  5. Speed improvements to the shuffle tool.
  6. Bug fixes to the p-value calculation in the fisher tool. Thanks to Brent Pedersen.
  7. Allow BED headers to start with chrom or chr
  8. Fixes to the "k-closest" functionality in the closest tool. Thanks to Neil Kindlon.
  9. Fixes to the output of the freqasc, freqdesc, distinct_sort_num and distinct_sort, and num_desc operations in the groupby tool. Thanks to @ghuls.
  10. Many minor bug fixes and compilation improvements from Luke Goodsell.
  11. Added the -fullHeader option to the maskfasta tool. Thanks to @ghuls.
  12. Many bug fixes and performance improvements from John Marshall.
  13. Fixed bug in the -N/-f behavior in subtract.
  14. Full support for .fai files as genome (-g) files.
  15. Many other minor bug fixes and functionality improvements.
Assets 3

@arq5x arq5x released this Jul 6, 2016 · 460 commits to master since this release

  1. Fixed a major memory leak when using -sorted. Thanks to Emily Tsang and Stephen Montgomery.
  2. Fixed a bug for BED files containing a single record with no newline. Thanks to @jmarshall.
  3. The getfasta tool includes name, chromosome and position in fasta headers when the -name option is used. Thanks to @rishavray.
  4. Fixed a bug that now forces the coverage tool to process every record in the -a file.
  5. Fixed a bug preventing proper processing of BED files with consecutive tabs.
  6. VCF files containing structural variants now infer SV length from either the SVLEN or END INFO fields. Thanks to Zev Kronenberg.
  7. Resolve off by one bugs when intersecting GFF or VCF files with BED files.
  8. The shuffle tool now uses roulette wheel sampling to shuffle to -incl regions based upon the size of the interval. Thanks to Zev Kronenberg and Michael Imbeault.
  9. Fixed a bug in coverage that prevented correct calculation of depth when using the -split option.
  10. The shuffle tool warns when an interval exceeds the maximum chromosome length.
  11. The complement tool better checks intervals against the chromosome lengths.
  12. Fixes for stddev, min, and max operations. Thanks to @jmarshall.
  13. Enabled stdev, sstdev, freqasc, and freqdesc options for groupby.
  14. Allow -s and -w to be used in any order for makewindows.
  15. Added new -bedOut option to getfasta.
  16. The -r option forces the -F value for intersect.
  17. Add -pc option to the genomecov tool, allowing coverage to be calculated based upon paired-end fragments.
Assets 3

@arq5x arq5x released this May 28, 2015 · 643 commits to master since this release

  1. The coverage tool now takes advantage of pre-sorted intervals via the -sorted option. This allows the coverage tool to be much faster,
    use far less memory, and report coverage for intervals in their original order in the input file.
  2. We have changed the behavior of the coverage tool such that it is consistent with the other tools. Specifically, coverage is now
    computed for the intervals in the A file based on the overlaps with the B file, rather than vice versa.
  3. The subtract tool now supports pre-sorted data via the -sorted option and is therefore much faster and scalable.
  4. The -nonamecheck option provides greater tolerance for chromosome labeling when using the -sorted option.
  5. Support for multiple SVLEN tags in VCF format, and fixed a bug that failed to process SVLEN tags coming at the end of a VCF INFO field.
  6. Support for reverse complementing IUPAC codes in the getfasta tool.
  7. Provided greater flexibility for "BED+" files, where the first 3 columns are chrom, start, and end, and the remaining columns are free-form.
  8. We now detect stale FAI files and recreate an index thanks to a fix from @gtamazian.
  9. New feature from Pierre Lindenbaum allowing the sort tool to sort files based on the chromosome order in a faidx file.
  10. Eliminated multiple compilation warnings thanks to John Marshall.
  11. Fixed bug in handling INS variants in VCF files.
Assets 3

@arq5x arq5x released this Feb 22, 2015 · 717 commits to master since this release

New features.

  1. Added -k option to the closest tool to report the k-closest features in one or more -b files.
  2. Added -fd option to the closest tool to for the reporting of downstream features in one or more -b files. Requires -D to dictate how "downstream" should be defined.
  3. Added -fu option to the closest tool to for the reporting of downstream features in one or more -b files. Requires -D to dictate how "downstream" should be defined.
  4. @lindenb added a new split tool that will split an input file into multiple sub files. Unlike UNIX split, it can balance the chunking of the sub files not just by number of lines, but also by total number of base pairs in each sub file.
  5. Added a new spacing tool that reports the distances between features in a file.
  6. @jayhesselberth added a -reverse option to the makewindows tool that reverses the order of the assigned window numbers.

Bug fixes.

  1. Fixed a bug that caused incorrect reporting of overlap for zero-length BED records. Thanks to @roryk.
  2. Fixed a bug that caused the map tool to not allow -b to be specified before -a. Thanks to @semenko.
  3. Fixed a bug in makewindows that mistakenly required -s with -n.
Assets 3
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