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1.7.0

1.6.0

1.5.0

1.4.0

  • Move cwl and examples into core cgpBigWig respository

1.3.0

  • Update to htslib 1.10.2
    • Required for PCAP-core to update to samtools 1.10 for new features
  • Update setup.sh to exec build/* scripts to reduce chance of divergence
  • Update Docker image to Ubuntu Focal (20.04) base.
  • Fix #33 (typo)

1.2.0

Add bam2bw -S/--scale-log10 to enable simple RPKM rescaling. Thanks to @shouldsee for these modifications.

1.1.0

Add docker build to allow internal large CI system to process. dockstore-cgpbigwig will be modified to base from here and only contain additional helpers and CWL.

1.0.4

  • Add checks to sam_iter_next to ensure result is checked for errors

1.0.3

Behaviour change

When the proper pair filter flag is used, this code now checks that the paired-end orientation is also used. This will mean that mate-pair orientation (F/F or R/R) will be rejected

  • Where a proper pair filter is used, now check for the correct paired-end orientation of F/R.
  • If this is not met the read is ignored
  • Added a -f filter of flags to include alongside the existing -F for exclude as per samtools style filtering for bam2bw, bam2bwbases and bam2bedgraph
  • NB this flag was used as the exclude in bam2bedgraph. The flags have now been switched.

1.0.2

  • Correct region parsing in bam2bw to cope woth GRCh38 contigs

1.0.1

  • Fix bam2bw. Single region string and -z caused header issues.

1.0.0

  • First full release
  • Add overlapping reads support to bam2bw, bam2bwbases and bam2bedgraph via commandline flag --overlap -a
    • If the same readname is encountered twice at a position it is considred an overlapping read pair.
    • Where the same base [ACGT] was encountered on each of the reads it will only be counted once. If a different base was encountered then the coverage count is incremented once for each base.
  • Updated License headers with new email address

0.5.0

  • Update to HTSlib 1.5 (for consistency across tools)
  • Update to libBigWig 0.4.2
  • Some README.md and INSTALL.md updates
    • Thanks go to jsmedmar for documentation contributions

0.4.4

  • Correct parseRegionString return type. Fixes #11.
  • Above change also fixes #12.

0.4.3

  • Updated libBigWig to 0.3.4 - fixes #10

0.4.2

  • Modified parsing of regions to enable names with : in (i.e. GRCh38)

0.4.1

  • Updated libBigWig to 0.3.1 - fixes issue with overflow in very large zoom levels

0.4.0

  • Added detectExtremeDepth code. Replaces functionality in PCAP-core detectExtremeDepth.pl

0.3.1

  • Changes HTSlib to 1.3.2 (bringing all stack in line)
  • Changed libBigWig archive get to use release rather than commit id (actually the same but harder to tell which release it is)

0.3.0

  • Changes to setup.sh to permit OSX installation

0.2.1

  • Corrections to logic

0.2.0

  • Added bedgraph to bw functionality via bg2bw

0.1.0

  • First release