In SAM_entry.pm, the parser doesn't support extended CIGAR strings, like those generated by minimap2 with the --eqx option. Here's a sample read:
m84173_240316_095122_s1/100012312/ccs/3767_4787 0 chr2 17601892 60 172S31=1X262=1X553= * 0 0 GACTCTTAGTTCCTAATTTGGTATTAATAGGAAATATGAATTATTATATACTTAATAAAATTTAGAATTCTGTTAAAATGCATGATCTCTATCAAATTTCCTATGCATCTACATGCAATAATGAACTCTTGGTTATTAATTTTTTTTTTCTTTTTGAGACGGAGTATCGCTCTGCCACCGCACTCCAGCCTGAATGACAGAGCAAGACTCCACCTAAAAAAAGTAAAAGAAAAAAAAGAGGAAGAATTAGCACATTTCTATTACAGAATTGGACTTGAACATGCAAAATCATGTCTGGATTTCTCAGTGAAAAGCTGTTTTACGTTAGTGGACTCTTCTAACATTTTGAAATGGTGATCTGGATTTGGGATCTGGCTATCACTGACCCACCTTGGGTCTGTGAATGACCAACTCACCTAGGTGGGAGTCAGTTACCCCTGCCCTCCAGTGGCCCATGGAGCACCTGTGGGAAGAAGGCTTTCTGTCTTACTGATTCTTCCATCTTTGGTGTCCAATTGGAAGGATTCCTGGGCCATTGACTGTTTCTCTCTGAGGGTTGTTATGAAGCTTGTGGCTCCATTCTCATGACTACTGTGATATTTCTGTGAATCTGACCCTGCCCTGAACTCCAGGTCAGCTTCTCCCCTCACAGGTGAAATCCAGTCCTATTATAACTGGGGGAGTGATAGACAGATTTTGGGCTATTTTACGACCAACTTTCCCTGTCTAAAATGTCAAAGCAGCCGGGTGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGATGCCGAGGCGGGTGGATCACCTGAGGCCAGGAGTTTGAGACCAGCCTGGCCAACACGGCGAAACTCTGTCTCTACTAAAGATATAAAAATTAGCCAGGTATGGTGCATGCCTGTAATCCCAGCTACTGGGGAGGCTGAGGCAGGAGAATTGCTTAAACCTAGGAGGCGGCAGTTGCATTGAGCCAAGATCACGCCATTGCACCCCAAGCTGGAAGACAGAGTAAGACTCCATCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII7IIIIIIIIII7IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIII<IIIIIIIIIIIIIIIIIII2IIIIIDIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIDIIII7IIIIIIIIIIIIIIIIIII7IIIIIIIIIIIIII<IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 ms:i:838 AS:i:838 nn:i:0 ts:A:+tp:A:P cm:i:208 s1:i:736 s2:i:0 de:f:0.0024 SA:Z:chr2,17749669,-,846S173M1S,60,0;rl:i:324
Characters like = and X in 172S31=1X262=1X553= are used instead of M, but that might be the only relevant difference. Something like jvarkit can easily preprocess the BAM to work here, but it would be great if this tool supported the notation.
In SAM_entry.pm, the parser doesn't support extended CIGAR strings, like those generated by minimap2 with the
--eqxoption. Here's a sample read:Characters like
=andXin172S31=1X262=1X553=are used instead ofM, but that might be the only relevant difference. Something like jvarkit can easily preprocess the BAM to work here, but it would be great if this tool supported the notation.