falir quantify fails on missing MD BAM tag

[diekhans]

Vikas encountered the following error:

(flair-dev) vpeddu@emerald:/private/groups/kimlab/vikas/nanopore/promethion/direct_cfrna/publication/flair$ flair quantify -r \
    read_manifest.tsv \
    -i drna.flair.collapse.trna.isoforms.fa \
    --threads 32 --output drna.flair.quantify.trna \
    --sample_id_only
Starting quantify...
Writing temporary files with prefixes similar to /data/tmp/tmp3br3w4mt
Step 1/3. Aligning sample drna1_b1, 1/4
Step 1/3. Aligning sample drna2_b1, 2/4
Step 1/3. Aligning sample drna3_b1, 3/4
Step 1/3. Aligning sample drna4_b1, 4/4
Step 2/3. Quantifying isoforms for sample drna1_b1: 1/4
Traceback (most recent call last):
  File "/private/groups/kimlab/vikas/HBEC/flair_split_tests/flair/src/flair/count_sam_transcripts.py", line 283, in <module>
    transcripttoreads = parsesam(args, transcripttoexons)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/groups/kimlab/vikas/HBEC/flair_split_tests/flair/src/flair/count_sam_transcripts.py", line 247, in parsesam
    mdtag = read.get_tag('MD')
            ^^^^^^^^^^^^^^^^^^
  File "pysam/libcalignedsegment.pyx", line 2507, in pysam.libcalignedsegment.AlignedSegment.get_tag
  File "pysam/libcalignedsegment.pyx", line 2546, in pysam.libcalignedsegment.AlignedSegment.get_tag
KeyError: "tag 'MD' not present"
Flair quantify took 0 minutes and 20 seconds

Flair took 0 minutes and 20 seconds and finished without issues.

[cafelton]

I independently discovered this recently, a quick fix is to just use --generate_map, but this definitely needs addressed in future versions

[diekhans]

debugging in now .. first reaction: "how did this ever work?" cafelton ***@***.***> writes:

…

cafelton left a comment (BrooksLabUCSC/flair#433) I independently discovered this recently, a quick fix is to just use --generate_map, but this definitely needs addressed in future versions -- Reply to this email directly or view it on GitHub: #433 (comment) You are receiving this because you were assigned. Message ID: ***@***.***>

[diekhans]

This was caused by minimap2 not being give the --MD flag if --output_bam was not specified.