BAM ignored

[physnano]

Hi Danny,

I recently had to rebuild my rna-framework environment and I am running into an issue with rf-count. The output is as follows:

[+] Making output directory...
[+] Guessing file types:

  Sample                     Type    5'-end trimming

  LIB6235932_align-sorted    BAM     Ignored

[+] Getting transcripts from reference, and building count table base structure...
[+] Inspecting SAM/BAM file headers...
[+] Assuming that provided SAM/BAM files are already sorted. Skipping sorting...
[+] Calculating per-base mutation counts and coverage. This may take a while...

  [-] Processing sample "LIB6235932_align-sorted" (PID: 11634)

[+] Statistics:

-1

[+] Cleaning up temporary files...
[+] All done.

The .fa reference has been processed with dos2unix:

cat -e gencode.v38.transcripts.pse_rem.fa | head -4
>ENST00000619216.1|ENSG00000278267.1|-|-|MIR6859-1-201|MIR6859-1|68|miRNA|$
TGTGGGAGAGGAACATGGGCTCAGGACAGCGGGTGTCAGCTTGCCTGACCCCCATGTCGCCTCTGTAG$
>ENST00000473358.1|ENSG00000243485.5|OTTHUMG00000000959.2|OTTHUMT00000002840.1|MIR1302-2HG-202|MIR1302-2HG|712|lncRNA|$
GTGCACACGGCTCCCATGCGTTGTCTTCCGAGCGTCAGGCCGCCCCTACCCGTGCTTTCTGCTCTGCAGACCCTCTTCCTAGACCTCCGTCCTTTGTCCCATCGCTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCCGCCAACCTCGGCTCCTCCGGGCAGCCCTCGCCCGGGGTGCGCCCCGGGGCAGGACCCCCAGCCCACGCCCAGGGCCCGCCCCTGCCCTCCAGCCCTACGCCTTGACCCGCTTTCCTGCGTCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCACCCCCCTTTAAGAATTCAATAGAGAAGCCAGACGCAAAACTACAGATATCGTATGAGTCCAGTTTTGTGAAGTGCCTAGAATAGTCAAAATTCACAGAGACAGAAGCAGTGGTCGCCAGGAATGGGGAAGCAAGGCGGAGTTGGGCAGCTCGTGTTCAATGGTTTTGTCCGCCTTCCCTGCCTCCTCTTCTGGGGGAGTTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCGCTGGCTGCAGCGTGTGGTCCCCTTACCAGAGTGAGGATGCGAAGAGAAGGTGGCTGTCTGCAAACCAGGAAGAGAGCCCTCACCGGGAACCCGTCCAGCTGCCACCTTGAACTTGGACTTCCAAGCCTCCAGAACTGTGAGGGATAAATGTAT$

And the Bam file does contain the MD field:

samtools view LIB6235931_align-sorted.bam | head -2
203f2077-66c7-4a13-b0c6-9a5f5722ad13    272     ENST00000473358.1|ENSG00000243485.5|OTTHUMG00000000959.2|OTTHUMT00000002840.1|MIR1302-2HG-202|MIR1302-2HG|712|lncRNA|   1  0473S55M2D61M3S  *       0       0       *       *       NM:i:2  ms:i:112        AS:i:112        nn:i:0  ts:A:+  tp:A:S  cm:i:32 s1:i:104        de:f:0.0085     MD:Z:55^TT61rl:i:0
e52b2a97-a72f-4fb7-96cc-414b527078ce    272     ENST00000473358.1|ENSG00000243485.5|OTTHUMG00000000959.2|OTTHUMT00000002840.1|MIR1302-2HG-202|MIR1302-2HG|712|lncRNA|   19 09S32M1I22M2D18M1I5M1I21M1I17M1D43M1D12M1D97M1D23M1I10M1D12M2D5M9D5M2D84M1D38M39S        *       0       0       *       *       NM:i:30 ms:i:383        AS:i:376        nn:i:0      ts:A:+  tp:A:S  cm:i:101        s1:i:368        de:f:0.0414     MD:Z:32C21^CT61^T1C41^C12^C97^G33^C12^AT5^AGAGAAGCC3C1^CA84^A0A37       rl:i:0

Anything else I should for in regards to the BAM that might be causing the issue?

[dincarnato]

Can you just issue a git pull? We erroneously pushed rf-count without removing a comment line, which caused the issue.