Andreas Wilm

782755 T>TAG predicted by LF2.15 on BAM files processed by both versions: $ zgrep 78275 *vcf.gz NC_000912_Mpneumoniae_comb.lf215.lf215.vcf.gz:NC_000912.1 782755 . T TAG 589 PASS DP=100;AF=0.200000;SB=3;DP4=41,40,8,12;INDEL;HRUN=1 NC_000912_Mpneumoniae_comb.lf3.lf215.vcf.gz:NC_000912.1 782755 . T TAG 589...

Looks like off by one error also for deletions. Unclear why this worked there. Needs full testing against LF215 on simulated data but see also https://github.com/andreas-wilm/lofreq3/issues/40

That would be nice to have!

That is wrong. For human it's luckily limited to duplicated alpha chains wrongly classified as beta. So at least it's easy to tell, which entries are wrong. ```python In [1]:...

This can happen if the wrong organism was passed to TCRrep()

- See /data/out/NC_000912_Mpneumoniae for LF2 vs LF3 - Missing: PPV vs Sens test script

Looks like it's viterbi: bwa mem -t 8 $reffa $fq1 $fq2 | samtools fixmate - - | lofreq viterbi -f $reffa -b - | samtools sort - -o SRR3924583.fm.vit.srt.bam; Already...

Offending sequence is SRR3924583.6445264. See `lofreq viterbi -f $reffa -b narrowddown.bam`. Sequence starts at 816,196 with cigar of 165M1D33M53S and according to mpileup ends on 816,394. Ref has 816,394 bases...

nimble build --lineDir:on --debuginfo` and `gdb lofreq` to give debug binary set args viterbi -f /data/refs/NC_000912_Mpneumoniae.fasta -b narrowddown.bam /home/ubuntu/.nimble/pkgs/cligen-1.4.0/cligen.nim(672) dispatchviterbi /home/ubuntu/lofreq3.git/src/lofreqpkg/viterbi.nim(218) viterbi /home/ubuntu/lofreq3.git/src/lofreqpkg/viterbi.nim(60) getRefContext /home/ubuntu/.choosenim/toolchains/nim-1.4.2/lib/system.nim(2496) []

Currently used in calling stage