[Brian Bushnell]

This bug has now been fixed as of 35.14, which I just uploaded. Filtering was essentially not being applied when the best site was filtered and inferior sites passed the minid yet did not have cigar strings (a very rare scenario). But, it works fine now.

-Brian

P.S. Without filtering, just with default parameters, you get this alignment:

M01472:214:000000000-AG0YC:1:2108:10755:20410 1:N:0:78  0       NC_001802DRannotations_(modified)   2154        35      46=1032D34=1X1=1X24=1X21=

...which in my view is better than any alternative, despite the long deletion.

[Brian Bushnell]

OK, that looks like a bug that is related to the "subfilter" setting. Without subfilter, it gets mapped here:

M01472:214:000000000-AG0YC:1:2108:10755:20410 1:N:0:78  0       NC_001802DRannotations_(modified)   3186        15      1=1X2=1X7=3X2=2X1=1X3=3X9=3X2=2X1=2X34=1X1=1X24=1X21=

With subfilter, that site gets killed because it has too many substitutions, so it chooses a different site that presumably has a worse alignment (more indels) but fewer than 15 substitutions, so it's still valid. However, for some reason the cigar string does not get generated for the new site. I'll find out why and fix that very soon. There's nothing wrong with your command.

-Brian

[GenoMax]

Looks like this (T's changed to U's): http://www.ncbi.nlm.nih.gov/nuccore/9629357/

[lankage]

>NC_001802DRannotations_(modified)
GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAUAAAGCUUGCCUUGAGUGCUUCAAGUAGUGUGUGCCCGUCUGUUGUGUGACUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGGGAAACCAGAGGAGCUCUCUCGACGCAGGACUCGGCUUGCUGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACUGGUGAGUACGCCAAAAAUUUUGACUAGCGGAGGCUAGAAGGAGAGAGAUGGGUGCGAGAGCGUCAGUAUUAAGCGGGGGAGAAUUAGAUCGAUGGGAAAAAAUUCGGUUAAGGCCAGGGGGAAAGAAAAAAUAUAAAUUAAAACAUAUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUCGCAGUUAAUCCUGGCCUGUUAGAAACAUCAGAAGGCUGUAGACAAAUACUGGGACAGCUACAACCAUCCCUUCAGACAGGAUCAGAAGAACUUAGAUCAUUAUAUAAUACAGUAGCAACCCUCUAUUGUGUGCAUCAAAGGAUAGAGAUAAAAGACACCAAGGAAGCUUUAGACAAGAUAGAGGAAGAGCAAAACAAAAGUAAGAAAAAAGCACAGCAAGCAGCAGCUGACACAGGACACAGCAAUCAGGUCAGCCAAAAUUACCCUAUAGUGCAGAACAUCCAGGGGCAAAUGGUACAUCAGGCCAUAUCACCUAGAACUUUAAAUGCAUGGGUAAAAGUAGUAGAAGAGAAGGCUUUCAGCCCAGAAGUGAUACCCAUGUUUUCAGCAUUAUCAGAAGGAGCCACCCCACAAGAUUUAAACACCAUGCUAAACACAGUGGGGGGACAUCAAGCAGCCAUGCAAAUGUUAAAAGAGACCAUCAAUGAGGAAGCUGCAGAAUGGGAUAGAGUGCAUCCAGUGCAUGCAGGGCCUAUUGCACCAGGCCAGAUGAGAGAACCAAGGGGAAGUGACAUAGCAGGAACUACUAGUACCCUUCAGGAACAAAUAGGAUGGAUGACAAAUAAUCCACCUAUCCCAGUAGGAGAAAUUUAUAAAAGAUGGAUAAUCCUGGGAUUAAAUAAAAUAGUAAGAAUGUAUAGCCCUACCAGCAUUCUGGACAUAAGACAAGGACCAAAGGAACCCUUUAGAGACUAUGUAGACCGGUUCUAUAAAACUCUAAGAGCCGAGCAAGCUUCACAGGAGGUAAAAAAUUGGAUGACAGAAACCUUGUUGGUCCAAAAUGCGAACCCAGAUUGUAAGACUAUUUUAAAAGCAUUGGGACCAGCGGCUACACUAGAAGAAAUGAUGACAGCAUGUCAGGGAGUAGGAGGACCCGGCCAUAAGGCAAGAGUUUUGGCUGAAGCAAUGAGCCAAGUAACAAAUUCAGCUACCAUAAUGAUGCAGAGAGGCAAUUUUAGGAACCAAAGAAAGAUUGUUAAGUGUUUCAAUUGUGGCAAAGAAGGGCACACAGCCAGAAAUUGCAGGGCCCCUAGGAAAAAGGGCUGUUGGAAAUGUGGAAAGGAAGGACACCAAAUGAAAGAUUGUACUGAGAGACAGGCUAAUUUUUUAGGGAAGAUCUGGCCUUCCUACAAGGGAAGGCCAGGGAAUUUUCUUCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCUUCAGGUCUGGGGUAGAGACAACAACUCCCCCUCAGAAGCAGGAGCCGAUAGACAAGGAACUGUAUCCUUUAACUUCCCUCAGGUCACUCUUUGGCAACGACCCCUCGUCACAAUAAAGAUAGGGGGGCAACUAAAGGAAGCUCUAUUAGAUACAGGAGCAGAUGAUACAGUAUUAGAAGAAAUGAGUUUGCCAGGAAGAUGGAAACCAAAAAUGAUAGGGGGAAUUGGAGGUUUUAUCAAAGUAAGACAGUAUGAUCAGAUACUCAUAGAAAUCUGUGGACAUAAAGCUAUAGGUACAGUAUUAGUAGGACCUACACCUGUCAACAUAAUUGGAAGAAAUCUGUUGACUCAGAUUGGUUGCACUUUAAAUUUUCCCAUUAGCCCUAUUGAGACUGUACCAGUAAAAUUAAAGCCAGGAAUGGAUGGCCCAAAAGUUAAACAAUGGCCAUUGACAGAAGAAAAAAUAAAAGCAUUAGUAGAAAUUUGUACAGAGAUGGAAAAGGAAGGGAAAAUUUCAAAAAUUGGGCCUGAAAAUCCAUACAAUACUCCAGUAUUUGCCAUAAAGAAAAAAGACAGUACUAAAUGGAGAAAAUUAGUAGAUUUCAGAGAACUUAAUAAGAGAACUCAAGACUUCUGGGAAGUUCAAUUAGGAAUACCACAUCCCGCAGGGUUAAAAAAGAAAAAAUCAGUAACAGUACUGGAUGUGGGUGAUGCAUAUUUUUCAGUUCCCUUAGAUGAAGACUUCAGGAAGUAUACUGCAUUUACCAUACCUAGUAUAAACAAUGAGACACCAGGGAUUAGAUAUCAGUACAAUGUGCUUCCACAGGGAUGGAAAGGAUCACCAGCAAUAUUCCAAAGUAGCAUGACAAAAAUCUUAGAGCCUUUUAGAAAACAAAAUCCAGACAUAGUUAUCUAUCAAUACAUGGAUGAUUUGUAUGUAGGAUCUGACUUAGAAAUAGGGCAGCAUAGAACAAAAAUAGAGGAGCUGAGACAACAUCUGUUGAGGUGGGGACUUACCACACCAGACAAAAAACAUCAGAAAGAACCUCCAUUCCUUUGGAUGGGUUAUGAACUCCAUCCUGAUAAAUGGACAGUACAGCCUAUAGUGCUGCCAGAAAAAGACAGCUGGACUGUCAAUGACAUACAGAAGUUAGUGGGGAAAUUGAAUUGGGCAAGUCAGAUUUACCCAGGGAUUAAAGUAAGGCAAUUAUGUAAACUCCUUAGAGGAACCAAAGCACUAACAGAAGUAAUACCACUAACAGAAGAAGCAGAGCUAGAACUGGCAGAAAACAGAGAGAUUCUAAAAGAACCAGUACAUGGAGUGUAUUAUGACCCAUCAAAAGACUUAAUAGCAGAAAUACAGAAGCAGGGGCAAGGCCAAUGGACAUAUCAAAUUUAUCAAGAGCCAUUUAAAAAUCUGAAAACAGGAAAAUAUGCAAGAAUGAGGGGUGCCCACACUAAUGAUGUAAAACAAUUAACAGAGGCAGUGCAAAAAAUAACCACAGAAAGCAUAGUAAUAUGGGGAAAGACUCCUAAAUUUAAACUGCCCAUACAAAAGGAAACAUGGGAAACAUGGUGGACAGAGUAUUGGCAAGCCACCUGGAUUCCUGAGUGGGAGUUUGUUAAUACCCCUCCCUUAGUGAAAUUAUGGUACCAGUUAGAGAAAGAACCCAUAGUAGGAGCAGAAACCUUCUAUGUAGAUGGGGCAGCUAACAGGGAGACUAAAUUAGGAAAAGCAGGAUAUGUUACUAAUAGAGGAAGACAAAAAGUUGUCACCCUAACUGACACAACAAAUCAGAAGACUGAGUUACAAGCAAUUUAUCUAGCUUUGCAGGAUUCGGGAUUAGAAGUAAACAUAGUAACAGACUCACAAUAUGCAUUAGGAAUCAUUCAAGCACAACCAGAUCAAAGUGAAUCAGAGUUAGUCAAUCAAAUAAUAGAGCAGUUAAUAAAAAAGGAAAAGGUCUAUCUGGCAUGGGUACCAGCACACAAAGGAAUUGGAGGAAAUGAACAAGUAGAUAAAUUAGUCAGUGCUGGAAUCAGGAAAGUACUAUUUUUAGAUGGAAUAGAUAAGGCCCAAGAUGAACAUGAGAAAUAUCACAGUAAUUGGAGAGCAAUGGCUAGUGAUUUUAACCUGCCACCUGUAGUAGCAAAAGAAAUAGUAGCCAGCUGUGAUAAAUGUCAGCUAAAAGGAGAAGCCAUGCAUGGACAAGUAGACUGUAGUCCAGGAAUAUGGCAACUAGAUUGUACACAUUUAGAAGGAAAAGUUAUCCUGGUAGCAGUUCAUGUAGCCAGUGGAUAUAUAGAAGCAGAAGUUAUUCCAGCAGAAACAGGGCAGGAAACAGCAUAUUUUCUUUUAAAAUUAGCAGGAAGAUGGCCAGUAAAAACAAUACAUACUGACAAUGGCAGCAAUUUCACCGGUGCUACGGUUAGGGCCGCCUGUUGGUGGGCGGGAAUCAAGCAGGAAUUUGGAAUUCCCUACAAUCCCCAAAGUCAAGGAGUAGUAGAAUCUAUGAAUAAAGAAUUAAAGAAAAUUAUAGGACAGGUAAGAGAUCAGGCUGAACAUCUUAAGACAGCAGUACAAAUGGCAGUAUUCAUCCACAAUUUUAAAAGAAAAGGGGGGAUUGGGGGGUACAGUGCAGGGGAAAGAAUAGUAGACAUAAUAGCAACAGACAUACAAACUAAAGAAUUACAAAAACAAAUUACAAAAAUUCAAAAUUUUCGGGUUUAUUACAGGGACAGCAGAAAUCCACUUUGGAAAGGACCAGCAAAGCUCCUCUGGAAAGGUGAAGGGGCAGUAGUAAUACAAGAUAAUAGUGACAUAAAAGUAGUGCCAAGAAGAAAAGCAAAGAUCAUUAGGGAUUAUGGAAAACAGAUGGCAGGUGAUGAUUGUGUGGCAAGUAGACAGGAUGAGGAUUAGAACAUGGAAAAGUUUAGUAAAACACCAUAUGUAUGUUUCAGGGAAAGCUAGGGGAUGGUUUUAUAGACAUCACUAUGAAAGCCCUCAUCCAAGAAUAAGUUCAGAAGUACACAUCCCACUAGGGGAUGCUAGAUUGGUAAUAACAACAUAUUGGGGUCUGCAUACAGGAGAAAGAGACUGGCAUUUGGGUCAGGGAGUCUCCAUAGAAUGGAGGAAAAAGAGAUAUAGCACACAAGUAGACCCUGAACUAGCAGACCAACUAAUUCAUCUGUAUUACUUUGACUGUUUUUCAGACUCUGCUAUAAGAAAGGCCUUAUUAGGACACAUAGUUAGCCCUAGGUGUGAAUAUCAAGCAGGA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[Brian Bushnell]

That should not happen... outm should only print mapped reads, except when processing paired data, in which case it will print unmapped reads if the mate is mapped. But according to the flag you are processing single-ended data and that read was mapped, so it should have a cigar string.

It's possible that this is a bug that I've fixed since v34.92, but I have no record of that in my changelog. So I'd like to try to replicate it to see if it's a current bug. I already have the read, but can you send me or direct me to the specific reference you are using?

Thanks,
Brian