Release 3.1.1

This release includes:

• New flags to write input sequence or reconstructed tr sequence to the vcf.
• Prints command line to vcf
• Allows for local alignment in wraparound DP.
• Updated alignment scoring matrices.

vamos-v3.0.6

This release fixes an off-by-1 error in sequences that are extracted.

A change in behavior is introduced as well that considers the tandem repeat sequence as starting at the base after the last non-TR base and ending one before the first non-TR base after the locus. This will include insertions that are mapped to the beginning or end of a locus, which is consistent with left-aligning of indels.

The consensus module was changed from abPOA to spoa.

The following options are added:
-Z Treat input as zero-based, half-open coordinates.
-E Print the reconstructed TR sequence based on the motif decomposition in the vcf genotype field.
-l Use local alignment to potentially trim start/end from annotations.

vamos-v3.0.4

This release fixes an off-by-1 error in sequences that are extracted.

A change in behavior is introduced as well that considers the tandem repeat sequence as starting at the base after the last non-TR base and ending one before the first non-TR base after the locus. This will include insertions that are mapped to the beginning or end of a locus, which is consistent with left-aligning of indels.

The consensus module was changed from abPOA to spoa.

The following options are added:
-Z Treat input as zero-based, half-open coordinates.
-E Print the reconstructed TR sequence based on the motif decomposition in the vcf genotype field.
-l Use local alignment to potentially trim start/end from annotations.

Documentation update

This updates the links for motif sets to the version 2.1 files.

Testing for haploid chrx

chrxtest-v8

Maybe last fix?

Adding debugging output and extra parameters

This adds parameters -m and -a for minimum coverage to call an SNV, and minimum alt coverage to call a het.

Output format and minor bug fix

Fixed double initialization of input bam header.
Modified VCF output so that STR/VNTR are output for SVTYPE according to input description.

Fixing bug in processing single sites

This fixes some IO errors processing single-site lists.

Adding extra code to handle haploid chrx

This adds some code to handle haploid chrx, and to handle noisy reads

Bug fix 2.1.5

This fixes a bug in vcf output.