NOTE: VCF output is significantly different now, and a len_affected column has been added to arcsv_out.tab output.

Updates mostly related to somatic SV calling.

• More tags in VCF output, including AF (allele fraction, for somatic calling). The VCF output should now be basically equivalent to the arcsv_out.tab output.
• You can now do haploid-only calling with the option -f “”
• Reference and gap files are now required arguments
• added output of affected reference length (len_affected, or EVENT_AFFECTED_LEN in VCF), which for complex SVs may differ from the naively computed size as distance from first to last breakpoint
• the --min_size option in filter-merge now uses the 'len_affected' column rather than the span of the SV; this is so, e.g., very small non-tandem duplications are still filtered appropriately.
• Renamed options in filter-merge for readability, and added options useful for somatic SV calling.

Main changes since last release:

• the discordant read clustering step is more stable, especially on lower coverage data or small chromosomes/regions
• soft-clipped read processing is much faster
• added back the 'filter_read_through' option, which attempts to find and exclude read pairs with insert size smaller than the typical read length
• other (small) bugfixes

First github release