Question: How to determine supplementary alignments`

[rob-p]

Hi,

I'm trying to replicate the output of minimap2 on the command line, and I'm having some difficulty determining when an alignment should be marked as supplementary. A minimal example is the following read

AGACCCTTCGTGGCACCCTCAAGGGCCACAACGGCTGGGTAAGCCAGTCGCTACTACCCCGAATTTGGACATGATCCTCGACCTCTCGAGACGCGGAAGATAAGACCCTCATCATTGGAAACGCCCCAGGGATAACAGCTAGTGGAATTCCACAGCGTGCTGGCGGGGTCCCTCCTTTGTTAGTGCTGTTGGTT
ATCTCGCATCCAATGGCCAGTTTGCCCTCTCAGGCTCCCGGGATGGAACCCTGAGCCTGGGATCTCACAACGGGCACCACCACGAGGCGATTTGTGGGCCATACAAGGATGCTGAGTGTGGCCTTCTCCTCAGACAACCGGCAGATTGTCTCTGGATCTCAGATAAGAAGCTATGGAATACCCTGGGTGTGTGC
AAATACACTGCCAGGAGCACTAGAGTGGGTGTCTTGTGTCCGCTCTCGCCCAACAGCAACCCTATCATCGTCTCCTGTGGCTGGGACAAGCTGGTCAAGGTATGGAACCTGGTAGTAACTGCAAAAGCTGAAGACCAACCACATTGGCCACACAGGTAGTGAACACGTGACTGTCTTCCAGATGGATCCCTCTG
TGCTTCTAGGCAAGATGGCCAGGCCATGTTGATCTCAACGAAGGCAACTTTACACGCTAGATGGTGGGGACTCCATCAACGCCCATGTGCTTCACTAACCGCTACTGGCTGTGTGCTGCACAGGACCCAGTACATCAAGAG

This read, when run with minimap2 -ax-ont -N100 and mapped against the human transcriptome produces the following records:

ENST00000511473_130_aligned_4365593_F_1_770_1   0       ENST00000507756.5       13      0       206S44M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M
4D37M1I9M3D24M1D12M2I8M1S  *       0       0       AGACCCTTCGTGGCACCCTCAAGGGCCACAACGGCTGGGTAAGCCAGTCGCTACTACCCCGAATTTGGACATGATCCTCGACCTCTCGAGACGCGGAAGATAAGACCCTCATCATTGGAAACGCCCCAGGGATAACAGCTAGT
GGAATTCCACAGCGTGCTGGCGGGGTCCCTCCTTTGTTAGTGCTGTTGGTTATCTCGCATCCAATGGCCAGTTTGCCCTCTCAGGCTCCCGGGATGGAACCCTGAGCCTGGGATCTCACAACGGGCACCACCACGAGGCGATTTGTGGGCCATACAAGGATGCTGAGTGTGGCCTTCTCCTCAGACAACCGGCA
GATTGTCTCTGGATCTCAGATAAGAAGCTATGGAATACCCTGGGTGTGTGCAAATACACTGCCAGGAGCACTAGAGTGGGTGTCTTGTGTCCGCTCTCGCCCAACAGCAACCCTATCATCGTCTCCTGTGGCTGGGACAAGCTGGTCAAGGTATGGAACCTGGTAGTAACTGCAAAAGCTGAAGACCAACCACA
TTGGCCACACAGGTAGTGAACACGTGACTGTCTTCCAGATGGATCCCTCTGTGCTTCTAGGCAAGATGGCCAGGCCATGTTGATCTCAACGAAGGCAACTTTACACGCTAGATGGTGGGGACTCCATCAACGCCCATGTGCTTCACTAACCGCTACTGGCTGTGTGCTGCACAGGACCCAGTACATCAAGAG &
,+'+&*()&'+&4-,4',+.()%'',*42.&/'+3)+)(-0((-)(+&)*,*&%()3+/)(()&'),.&&0$*./4()*'30(*0'($(&-&%$''&(%+0)*+,*+/%+-79)2*+%,&/&$&(%/8)1;05',)((,;%&..,3,%&2)2'*1)'':'%.)*(-'+0+*(+*((+,&*,-)+/*-+-%,)'(
').+'$#+*#'#(-(.,***,'.246+(,'0+)1,#*$**(+,*))*0-4./(.7'(1,/(/+%%-&+,)&)'/)-/00*)+-%+>*')..2(&')()*+&)(60&(+*2'*-'&+),%'+),>&.%))*%(%).*+(*)/+-*13&11(/))+')*++'+)'/%%%)))%%0,%-*)*7((*%0)(---'&2*
26-+%:(%.(8&1*'()4%&(1+(73.1%+)''//'2*(2-0%/+*.+./,8),,%%(&(.(*()(*'+0+/'',-)'-'/2+&/,?/*)(,)/,'.-&--%(+&+1((*,$%),)+**('')&('/2')*'&2',3&0++++-))+%+*&$')4+1&0(,((.&*&+/'''+))&0$-)-&*))1&*&',+$+
(1('')+.,2,)+%+%,-(..&/)2)('*0,.'.''+)&,,)/+,/')(-+&/)())(1.'*15+)(**1))','*)+'.%+4(-00+(/*,0$)',)1-(((.,1(%+'+04$',(--+&&-(',&,,&*.5&*,.-1'    NM:i:59      ms:i:791        AS:i:764        nn:i:
0  tp:A:P  cm:i:32 s1:i:260        s2:i:300        de:f:0.0637     SA:Z:ENST00000511566.5,95,+,1S596M27D126S,60,83;        rl:i:0
ENST00000511473_130_aligned_4365593_F_1_770_1   256     ENST00000512805.6       121     0       1S46M1D19M3D12M3D2M1I7M9I18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1
D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M1S       *       0       0       *       *       NM:i:102        ms:i:998        AS:i:952        nn:i:0       tp
:A:S  cm:i:37 s1:i:300        de:f:0.0827     rl:i:0
ENST00000511473_130_aligned_4365593_F_1_770_1   256     ENST00000508682.5       117     0       1S46M1D19M3D12M3D2M1I7M9I18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M117D3
M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M1S     *       0       0       *       *       NM:i:214        ms:i:989        AS:i:825        nn:i:0       tp
:A:S  cm:i:37 s1:i:285        de:f:0.0827     rl:i:0
ENST00000511473_130_aligned_4365593_F_1_770_1   256     ENST00000504325.5       104     0       1S46M1D19M3D12M3D2M1I7M9I18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D15M4D32M1D6M2D51M1D6M6D38M1D4M
5D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M1S  *       0       0       *       *       NM:i:106        ms:i:989        AS:i:940        nn:i:0       tp
:A:S  cm:i:34 s1:i:286        de:f:0.0839     rl:i:0
ENST00000511473_130_aligned_4365593_F_1_770_1   256     ENST00000511473.5       131     0       1S46M1D19M3D12M3D2M1I15M3D19M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M5D3M
1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M1S      *       0       0       *       *       NM:i:99 ms:i:1001       AS:i:964        nn:i:0  tp:A:S       cm
:i:37 s1:i:297        de:f:0.0857     rl:i:0
ENST00000511473_130_aligned_4365593_F_1_770_1   256     ENST00000376817.8       204     0       219S6M1D25M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4
D17M4D37M1I9M3D24M1D12M2I8M1S      *       0       0       *       *       NM:i:60 ms:i:759        AS:i:732        nn:i:0  tp:A:S  cm:i:36 s1:i:268        de:f:0.067      rl:i:0
ENST00000511473_130_aligned_4365593_F_1_770_1   256     ENST00000510199.5       452     0       97S18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M
2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D25M22S     *       0       0       *       *       NM:i:78 ms:i:864        AS:i:834        nn:i:0  tp:A:S  cm:i:32 s1:i:260        de:f:0.0799  rl
:i:0
ENST00000511473_130_aligned_4365593_F_1_770_1   256     ENST00000502844.5       817     0       98S17M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M
2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D25M22S     *       0       0       *       *       NM:i:78 ms:i:862        AS:i:832        nn:i:0  tp:A:S  cm:i:32 s1:i:260        de:f:0.08    rl
:i:0
ENST00000511473_130_aligned_4365593_F_1_770_1   256     ENST00000507000.5       89      0       99S16M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M
2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D24M70S      *       0       0       *       *       NM:i:72 ms:i:792        AS:i:764        nn:i:0  tp:A:S  cm:i:30 s1:i:243        de:f:0.08   rl:i:0
ENST00000511473_130_aligned_4365593_F_1_770_1   2048    ENST00000511566.5       95      60      1H46M1D19M3D12M3D2M1I7M9I18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1
D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D8M126H      *       0       0       GACCCTTCGTGGCACCCTCAAGGGCCACAACGGCTGGGTAAGCCAGTCGCTACTACCCCGAATTTGGACATGATCCTCGACCTCTCGAGACGCGGAAGATAAGACCCTCAT
CATTGGAAACGCCCCAGGGATAACAGCTAGTGGAATTCCACAGCGTGCTGGCGGGGTCCCTCCTTTGTTAGTGCTGTTGGTTATCTCGCATCCAATGGCCAGTTTGCCCTCTCAGGCTCCCGGGATGGAACCCTGAGCCTGGGATCTCACAACGGGCACCACCACGAGGCGATTTGTGGGCCATACAAGGATGC
TGAGTGTGGCCTTCTCCTCAGACAACCGGCAGATTGTCTCTGGATCTCAGATAAGAAGCTATGGAATACCCTGGGTGTGTGCAAATACACTGCCAGGAGCACTAGAGTGGGTGTCTTGTGTCCGCTCTCGCCCAACAGCAACCCTATCATCGTCTCCTGTGGCTGGGACAAGCTGGTCAAGGTATGGAACCTGG
TAGTAACTGCAAAAGCTGAAGACCAACCACATTGGCCACACAGGTAGTGAACACGTGACTGTCTTCCAGATGGATCCCTCTGTGCTTCTAGGCAAGA   ,+'+&*()&'+&4-,4',+.()%'',*42.&/'+3)+)(-0((-)(+&)*,*&%()3+/)(()&'),.&&0$*./4()*'30(*0'($(&-&%$
''&(%+0)*+,*+/%+-79)2*+%,&/&$&(%/8)1;05',)((,;%&..,3,%&2)2'*1)'':'%.)*(-'+0+*(+*((+,&*,-)+/*-+-%,)'(').+'$#+*#'#(-(.,***,'.246+(,'0+)1,#*$**(+,*))*0-4./(.7'(1,/(/+%%-&+,)&)'/)-/00*)+-%+>*')..2(&
')()*+&)(60&(+*2'*-'&+),%'+),>&.%))*%(%).*+(*)/+-*13&11(/))+')*++'+)'/%%%)))%%0,%-*)*7((*%0)(---'&2*26-+%:(%.(8&1*'()4%&(1+(73.1%+)''//'2*(2-0%/+*.+./,8),,%%(&(.(*()(*'+0+/'',-)'-'/2+&/,?/*)(,)/
,'.-&--%(+&+1((*,$%),)+**('')&('/2')*'&2',3&0++++-))+%+*&$')4+1&0(,((.&*&+/'''+))&0$-)-&*))1&*&',+$+(1('')+.,2,)+%   NM:i:83 ms:i:822        AS:i:786    nn:i:0   tp:A:P  cm:i:32 s1:i:254

As you can see, the last of these is supplementary. However, when using the minimap2-rs bindings see this issue here, no supplementary alignments are produced --- though the total number of mappings and the targets are the same. Likewise, mappy doesn't have a field for supplementary alignments, but the results from mappy are as follows:

1       722     +       ENST00000512805.6       1140    120     878     677     779     0       tp:A:P  ts:A:.  cg:Z:46M1D19M3D12M3D2M1I7M9I18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51
M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M   cs:Z::41*cg:4-a:14*ca:1*gt:2-ccc:12-ctc:2+a:7+agacgcgga:10*ac:7-g:7*tg*gc*ac:8-gag:1*ca:2*
ag:3+g:19-c*tg:8*ac:3-cca:11*ac:2+t:10+g:1+a:2*ac*ga:26*tc:14*ca:2-ct:47-c:6-tg:22*ta:28-g:6-aaccat*cg:37-t:4-gatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:6-g:17-atgg:17-ac
ac:24*at*tc:11+a:9-gcc:24-c:6*ca:5+ta:8 MD:Z:41C4^A14C1G2^CCC12^CTC19A7^G7T0G0A8^GAG1C2A22^C0T8A3^CCA11A15A0G26T14C2^CT47^C6^TG22T28^G6^AACCAT0C37^T4^GATGA3^C4^C22^T10^CAG59C39^C2^T0C7^G10^C25^G
G6^G17^ATGG17^ACAC24A0T20^GCC24^C6C13
206     722     +       ENST00000507756.5       889     12      564     500     559     0       tp:A:S  ts:A:.  cg:Z:44M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D
25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M        cs:Z::26*tc:14*ca:2-ct:47-c:6-tg:22*ta:28-g:6-aaccat*cg:37-t:4-gatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:6-g:17-atgg:17-a
cac:24*at*tc:11+a:9-gcc:24-c:6*ca:5+ta:8        MD:Z:26T14C2^CT47^C6^TG22T28^G6^AACCAT0C37^T4^GATGA3^C4^C22^T10^CAG59C39^C2^T0C7^G10^C25^GG6^G17^ATGG17^ACAC24A0T20^GCC24^C6C13
1       722     +       ENST00000508682.5       1208    116     986     677     891     0       tp:A:S  ts:A:.  cg:Z:46M1D19M3D12M3D2M1I7M9I18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51
M1D6M6D38M1D4M117D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M cs:Z::41*cg:4-a:14*ca:1*gt:2-ccc:12-ctc:2+a:7+agacgcgga:10*ac:7-g:7*tg*gc*ac:8-gag:1*ca:2*
ag:3+g:19-c*tg:8*ac:3-cca:11*ac:2+t:10+g:1+a:2*ac*ga:26*tc:14*ca:2-ct:47-c:6-tg:22*ta:28-g:6-aaccat*cg:37-t:4-gctggagtgcagtagtgcgatctcggctcactgcaagctctgcttcccgggttcacgccattctcctgcctcagcctcccgagt
cgctgggactacaggcgcctgccatcaggatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:6-g:17-atgg:17-acac:24*at*tc:11+a:9-gcc:24-c:6*ca:5+ta:8 MD:Z:41C4^A14C1G2^CCC12^CTC19A7^G7T0G0A8^G
AG1C2A22^C0T8A3^CCA11A15A0G26T14C2^CT47^C6^TG22T28^G6^AACCAT0C37^T4^GCTGGAGTGCAGTAGTGCGATCTCGGCTCACTGCAAGCTCTGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTCGCTGGGACTACAGGCGCCTGCCATCAGGATGA3^C4^C22^
T10^CAG59C39^C2^T0C7^G10^C25^GG6^G17^ATGG17^ACAC24A0T20^GCC24^C6C13
1       722     +       ENST00000504325.5       1098    103     865     677     783     0       tp:A:S  ts:A:.  cg:Z:46M1D19M3D12M3D2M1I7M9I18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D15M4D32M1D6
M2D51M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M      cs:Z::41*cg:4-a:14*ca:1*gt:2-ccc:12-ctc:2+a:7+agacgcgga:10*ac:7-g:7*tg*gc*ac:8-gag
:1*ca:2*ag:3+g:19-c*tg:8*ac:3-cca:11*ac:2+t:10+g:1+a:2*ac*ga:26*tc:14*ca:2-ct:15-gcaa:32-c:6-tg:22*ta:28-g:6-aaccat*cg:37-t:4-gatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:6
-g:17-atgg:17-acac:24*at*tc:11+a:9-gcc:24-c:6*ca:5+ta:8 MD:Z:41C4^A14C1G2^CCC12^CTC19A7^G7T0G0A8^GAG1C2A22^C0T8A3^CCA11A15A0G26T14C2^CT15^GCAA32^C6^TG22T28^G6^AACCAT0C37^T4^GATGA3^C4^C22^T10^CAG
59C39^C2^T0C7^G10^C25^GG6^G17^ATGG17^ACAC24A0T20^GCC24^C6C13
1       722     +       ENST00000511473.5       1150    130     900     683     782     0       tp:A:S  ts:A:.  cg:Z:46M1D19M3D12M3D2M1I15M3D19M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D5
1M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M  cs:Z::41*cg:4-a:14*ca:1*gt:2-ccc:12-ctc:2+a:9*ga*tc*ag:3-act:11*ac:7-g:7*tg*gc*ac:8-gag:1*
ca:2*ag:3+g:19-c*tg:8*ac:3-cca:11*ac:2+t:10+g:1+a:2*ac*ga:26*tc:14*ca:2-ct:47-c:6-tg:22*ta:28-g:6-aaccat*cg:37-t:4-gatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:6-g:17-atgg:
17-acac:24*at*tc:11+a:9-gcc:24-c:6*ca:5+ta:8    MD:Z:41C4^A14C1G2^CCC12^CTC11G0T0A3^ACT11A7^G7T0G0A8^GAG1C2A22^C0T8A3^CCA11A15A0G26T14C2^CT47^C6^TG22T28^G6^AACCAT0C37^T4^GATGA3^C4^C22^T10^CAG59C
39^C2^T0C7^G10^C25^GG6^G17^ATGG17^ACAC24A0T20^GCC24^C6C13
219     722     +       ENST00000376817.8       965     203     743     487     547     0       tp:A:S  ts:A:.  cg:Z:6M1D25M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D1
0M1D25M2D6M1D17M4D17M4D37M1I9M3D24M1D12M2I8M    cs:Z::6-g:7*tc:14*ca:2-ct:47-c:6-tg:22*ta:28-g:6-aaccat*cg:37-t:4-gatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:6-g:17-atgg:1
7-acac:24*at*tc:11+a:9-gcc:24-c:6*ca:5+ta:8     MD:Z:6^G7T14C2^CT47^C6^TG22T28^G6^AACCAT0C37^T4^GATGA3^C4^C22^T10^CAG59C39^C2^T0C7^G10^C25^GG6^G17^ATGG17^ACAC24A0T20^GCC24^C6C13
97      701     +       ENST00000510199.5       1100    451     1096    576     654     0       tp:A:S  ts:A:.  cg:Z:18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1
D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D25M   cs:Z::10*ac:7-g:7*tg*gc*ac:8-gag:1*ca:2*ag:3+g:19-c*tg:8*ac:3-cca:11*ac:2+t:10+g:1+a:2*ac*ga:26*tc:14*ca:2-ct:47-c:6-tg:22
*ta:28-g:6-aaccat*cg:37-t:4-gatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:6-g:17-atgg:17-acac:24*at*tc:11+a:9-gcc:25       MD:Z:10A7^G7T0G0A8^GAG1C2A22^C0T8A3^CCA11A15A0G26T
14C2^CT47^C6^TG22T28^G6^AACCAT0C37^T4^GATGA3^C4^C22^T10^CAG59C39^C2^T0C7^G10^C25^GG6^G17^ATGG17^ACAC24A0T20^GCC25
98      701     +       ENST00000502844.5       1460    816     1460    575     653     0       tp:A:S  ts:A:.  cg:Z:17M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1
D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D37M1I9M3D25M   cs:Z::9*ac:7-g:7*tg*gc*ac:8-gag:1*ca:2*ag:3+g:19-c*tg:8*ac:3-cca:11*ac:2+t:10+g:1+a:2*ac*ga:26*tc:14*ca:2-ct:47-c:6-tg:22*
ta:28-g:6-aaccat*cg:37-t:4-gatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:6-g:17-atgg:17-acac:24*at*tc:11+a:9-gcc:25        MD:Z:9A7^G7T0G0A8^GAG1C2A22^C0T8A3^CCA11A15A0G26T1
4C2^CT47^C6^TG22T28^G6^AACCAT0C37^T4^GATGA3^C4^C22^T10^CAG59C39^C2^T0C7^G10^C25^GG6^G17^ATGG17^ACAC24A0T20^GCC25
99      653     +       ENST00000507000.5       685     88      681     529     601     0       tp:A:S  ts:A:.  cg:Z:16M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51M1D6M6D38M1D4M5D3M1D4M1
D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D6M1D17M4D17M4D24M    cs:Z::8*ac:7-g:7*tg*gc*ac:8-gag:1*ca:2*ag:3+g:19-c*tg:8*ac:3-cca:11*ac:2+t:10+g:1+a:2*ac*ga:26*tc:14*ca:2-ct:47-c:6-tg:22*ta:28-g:
6-aaccat*cg:37-t:4-gatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:6-g:17-atgg:17-acac:24    MD:Z:8A7^G7T0G0A8^GAG1C2A22^C0T8A3^CCA11A15A0G26T14C2^CT47^C6^TG22T28^G6^AACCAT0C3
7^T4^GATGA3^C4^C22^T10^CAG59C39^C2^T0C7^G10^C25^GG6^G17^ATGG17^ACAC24
1       597     +       ENST00000511566.5       825     94      717     558     641     0       tp:A:S  ts:A:.  cg:Z:46M1D19M3D12M3D2M1I7M9I18M1D18M3D8M1I19M1D13M3D14M1I10M1I1M1I48M2D47M1D6M2D51
M1D6M6D38M1D4M5D3M1D4M1D22M1D10M3D59M2I8M2I32M1D2M1D8M1D10M1D25M2D8M    cs:Z::41*cg:4-a:14*ca:1*gt:2-ccc:12-ctc:2+a:7+agacgcgga:10*ac:7-g:7*tg*gc*ac:8-gag:1*ca:2*ag:3+g:19-c*tg:8*ac:3-cca:11*ac:
2+t:10+g:1+a:2*ac*ga:26*tc:14*ca:2-ct:47-c:6-tg:22*ta:28-g:6-aaccat*cg:37-t:4-gatga:3-c:4-c:22-t:10-cag:59+ta*cg:7+aa:32-c:2-t*cg:7-g:10-c:25-gg:8      MD:Z:41C4^A14C1G2^CCC12^CTC19A7^G7T0G0A8^G
AG1C2A22^C0T8A3^CCA11A15A0G26T14C2^CT47^C6^TG22T28^G6^AACCAT0C37^T4^GATGA3^C4^C22^T10^CAG59C39^C2^T0C7^G10^C25^GG8

What can I do to determine which mappings minimap2, when invoked from the command line, would mark as supplementary? I'm most concerned about getting this right in minimap2-rs, where we should have access to most of the raw data structures filled in by the mm_map function.

Thanks!
Rob

[rob-p]

Ok, so I figured it out. These are "corner cases" where the tie-breaking via hashing the query name makes a difference, but the minimap2-rs wrapper (and mappy, I believe) don't accept the read/query name. I resolved this by adding a function to minimap2-rs that also accepts the query name and now the output matches minimap2 when run from the command line. Perhaps it's worthwhile having a similar ability in mappy? Anyway, I'll close this as resolved since I figured it out.