v2.1.1

SVDSS version 2.1.0

• (bugfix) Output SFS batches only once (depending on number of reads and --bsize, some batches were output twice)
• (bugfix) Fix check on SV length
• (change) Default to 0/1 genotypes. We still suggest genotyping the calls with an external genotyper

v2.1.0

SVDSS version 2.1.0

• change to smoother: alignment accuracy (old --accq) is now autocomputed using the first 10k primary alignments and then selecting the 98th percentile (see --accp)
• move to robebwt3
• update abpoa to v1.5.3
• use ksw2 to realign consensus
• remove genotyper (use kanpig if needed)
• new script (run_svdss) to run the entire pipeline (including optional genotyping)

v2.0.0

SVDSS v2:

• haplotags (if present in the input BAM file) can be used to guide subclustering and SV calling
• bug fixes
• changes to CLI

v2.0.0-alpha.3

Third alpha release for SVDSS2:

• rename fasta/q CLI option to fastx
• CLI option to filter based on mapping quality
• CLI option to remove 0/0 calls
• CLI option to ignore haplotag information

v2.0.0-alpha.2

Second alpha release for SVDSS2:

• fixes a bug in pingpong (small batches were potentially skipped)

v2.0.0-alpha.1

First alpha release for SVDSS2

v1.0.5-fix

Bug fixing for v1.0.5:

• Multiple extended SFSs when too close
• Missing first base in insertion alleles
• Segmentation fault in clipped mode (#24)

This is the last patch for SVDSS v1. We will move to SVDSS2

v1.0.5

Patch over v1.0.4:

• bug fixing
• various heuristic improvements

Please check PR #18 for more info.

v1.0.4

Patch over v1.0.3:

• updates abpoa to v1.4.1 to solve "random" segfaults - see #12
• removes filtering of "unwanted" chromosomes (i.e. ALT contigs. User should take care of it) - see #10
• fixes search over a fastq
• improves cli

v1.0.3

Patch over v1.0.2:

• fixes portable compilation (removes -march=native)
• fixes a bug in assemble mode
• small help improvements