v.0.18.3

2023-02-14 Youri Hoogstrate v0.18.3

• when provided the appropriate discordant reads (i.e. no cannonical reads) from the master bam, dr-disco fix should be able to correctly fix those. Detailed bug report by Marcel Smid, thanks! STAR reports HI:i:-tags in the master bam different from chimeric.out files.
• got rid of fuma dependency

v0.18.2

• strict mode for dr-disco bam-extract querying only targeted chromosomes/reference_names

v0.18.0

• Python3

v0.16.3

• Fixes SA:Z: tags by swapping strand information with CIGAR and by replacing chromosomes to = if they are the same. This will solve prevent dissapearing pannels in IGV 2.4.1 - 2.4.10. A backwards incompatibility fix has directly been implemented and the changes do not affect the outcome and only improve visualization.
• Trigger Exception in dr-disco integrate when position of break is out of bound relative to --fasta.

v0.16.2

• Improves classification filters based on outliers

v0.16.1

• Improves filter for extremely high expressed exonic fusions (reduces false negative ratio)

v0.16.0

• Adds the exons before the break and exons after the break to the integrate results. Remark that the offset to match an exon is [-2,+2] because STAR may introduce slight offset errors.
• Fixes bug in integrate where rather similar fusions in opposite strands were still bundled together.

v0.15.2

• Makes mismatches per base classification more stringent unless --ffpe is used. Using --ffpe the old behaviour is preserved.

The CLI argument itself says:

--ffpe    Lowers the threshold for the relative amount of
         mismatches, as often found in FFPE material.
         Note that enabling this option will
         consequently result in more false positives.

v0.15.1

• Additional filter

v0.15.0

• Bugfix resulting in higher number of detected frame shifts
• dr-disco integrate --fasta <fa file> provides edit distance to canonical splice junction motif (quick impementation)

No changes to detection or to classification, so performance (TP/FP ratios etc.) will not be affected