v0.7.1

Bug fix to allow '>' characters inside a quoted Description field

v0.7.0

This release incorporates the following changes from @brentp:

• Add an option to allow switching to use the 95% confidence interval if the full confidence interval is too large.
• Only load necessary data from CRAM files. This increases svtyper speed when reading from a CRAM file.

v0.6.1

This release incorporates the following changes:

• Fix BND warning so that it only triggers when valid as opposed to every time the program runs.

v0.6.0

This release incorporates the following changes:

• Only utilize soft clip evidence to supplement paired end or split read evidence for the SV. Soft clips are no longer counted if they are the only evidence for an SV.
• Add a warning in svtyper classic if BNDs are not genotyped due to missing mates.

v0.5.2

This fixes an error where the version string wasn't properly set in v0.5.1. Functionality is otherwise identical from v0.5.1

v0.5.1

This release incorporates the following changes:

• Suppress status messages in svtyper classic regarding the reading and construction of the library distributions by default. These status messages can be re-enabled by using the newly added --verbose option.

v0.5.0

This release incorporates the following changes:

• Duplication genotyping model has been adjusted. The new model is more sensitive and should better reflect genotyping uncertainty.
• Genotype quality calculations have been improved.

If you have filtering scripts relying on genotype quality (and/or site quality for DUPs) you may need to recalibrate them before applying to this version.

Special thanks to @kmsteinberg for sharing instances where the previous duplication calling settings were causing real variants to be missed.

v0.1.4

• Set --max_reads to unlimited by default, as a max of 1000 was conflicting with some of our pipeline steps

v0.1.3

• New default behavior clears existing QUAL scores. (Use the -q flag to iterate existing QUAL field from input VCF)
• Limit number of reads to 1000 at each variant site (--max_reads), to prevent slow processing time in high-depth, repetitive regions (thanks to @brentp)
• add argument (-T) for optional reference FASTA when reading CRAM files. (This prevents automatically downloading of the reference cache)
• Throw error if SVTYPE missing from VCF file

v0.1.2

• Fixes a bug in building insert size distributions from CRAM files