Daniel Cameron comments

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                                            Daniel Cameron

Deletion at the end of the alignment

The deletion can also be at the start of the cigar. Be aware that bwa defines the alignment start as the position of the start of the deletion, whereas the...

Obtaining primary alignment position from secondary alignment?

Secondary or supplementary alignment? Supplementary alignment (aka split read alignments) locations should use the SA tag. There is no spec-defined equivalent to record the multiple different alternative read alignments (ie...

Clarify IMPRECISE/CIPOS descriptions

Resolved in 4.4

spec for short tandem repeat varaints

Implemented in #676

Expanding the Phasing notation for triploid+ genotypes

In 4.4

Clarify the relationship between CNV and DEL/DUP structural variation types

>either a claim of overall copy number gain, or a claim of a copy number increase of at least one allele 4.4 has INFO CN = ASCN and FORMAT CN...

Clarify the validity of BND as first-level symbolic alleles

Fixed in 4.4

Output files are empty

I managed to work around this issue by rerunning `Weaver PLOIDY` with `-r 1` then running `Weaver LITE` with `-r 0` so it wouldn't overwrite `tempread` with a file contains...

Segmentation fault

I have the same problem and it is not a user error. Uncommenting main.cpp:250 indicates that BIN is set to an empty string. Weaver is in fact attempting to call...

Can't read or write gzipped BCFs

FYI: in VCF version 4.4, the following line (which has been in the VCF specifications since at least 2013) will be removed from the BCF portion of the specification: ```...