* Deletions now count as hard clipped bases in order to recover the original alignment start of a clipped read.
* Insertions do not count as hard clipped bases for the same reason.
* This created a bug in the previous cigar cleaning function. Fixed.
-We now assign a functional class (nonsense, missense, silent, or none) to each SnpEff effect, and add a
SNPEFF_FUNCTIONAL_CLASS annotation to the INFO field of the output VCF.
-Effects are now prioritized according to both biological impact and functional class, instead of impact only.
-Many of SnpEff's "low-impact" effects are now classified as "modifiers" with lower priority than every
other effect. This includes such "effects" as DOWNSTREAM, UPSTREAM, INTRON, GENE, EXON, and others that
really describe the location of the variant rather than its biological effect.
This code will be short-lived (likely 1.2-only), as the next version of SnpEff will include most of these
features directly.
Checking this change into Stable+Unstable instead of Unstable because the current functional class stratification
in VariantEval is basically broken and urgently needs to be fixed for production purposes.
Insertions and deletions now have a separate threshold to trigger a variant region. The default is 0.01, meaning that every site with at least 1 in a 100 insertion/deletion will be triggered as a variant region.
The mapping quality of the consensus reads is the average of the RMS of all reads that contributed to the consensus, weighted according to the size of the contribution of each read.
if soft clipped bases were after a hard clipped section of the read, the hard clip was clipping the left soft clip tail as if it were a right tail. Mayhem.
- Filter out per-library information in per-sample metrics so that our aggregator doesn't crash out
while we figure out how to handle data per-library rather than per-sample.
- Compare preQC metrics for custom captures to all exome data. Note that not every metric makes sense
when compared to every other bait set, so a warning message is emitted on the summary page.
* Hard clipped Cigar now includes all insertions that were hard clipped and not the deletions.
* The alignment start is now recalculated according to the new hard clipped cigar representation
Khalid Shakir
Mauricio Carneiro
David Roazen
Matt Hanna
Mark DePristo
Eric Banks