v0.3.1

New release for DOI.

v0.3.0

• Add a few new wrappers to lumpy, the latest and recommended is smoove
• Add CRAM support
• Many improvements to the extraction of paired-end and split-read alignments from source BAM
• Fix SV evidence display with the -e option

v0.2.13

Small update to the VCF header output to include the BD info field.

v0.2.12

In general, this version should be more robust to BAMs with funny CIGAR strings and lumpyexpress also be more robust.

Here is a summary of the changes since 0.2.11.

• Enable BAM streaming to bamfilterrg for samtools (chapmanb)
• Fix for streaming to pysam in bamfilterrg (chapmanb)
• fix mem leaks
• add cnvnator to bedpe
• fix issue with zero len read
• use gawk instead of awk, since some versions of awk do not support i=1;i<=k;++i style for loops
• many fixes to lsort and lmerge
• Add translocations to BEDPE
• get rid of -M in lumpyexpress

v0.2.11

Fix test cases.

v0.2.10

Fixed test data

v0.2.9

• Add the ability to handle multiple read groups within a single BAM
• Fix an issue with the right-hand PDF when using the "-P" option
• Remove a check that ignored split reads flagged as paired

v0.2.8

Added a check to make sure the CIGAR string has at least 1 M.

v0.2.7

Remove a debug statement.

v0.2.6

Documentation updates and a split-read interchromosomal bug fix.