FATAL: add_link when running matlock bam2 counts #7
Description
Hi,
We're getting an error FATAL:add_link running matlock from commit 9fe3fdd, as follows:
$ matlock bam2 counts my.bam links.out
INFO: converting bam to lachesis on my.bam
INFO: detected bam filetype
INFO: reading file "my.bam"
FATAL: add_link
Here's the body of my.bam (this is a subset of a larger HiC BAM), happy to send it for troubleshooting if that helps
GWNJ-0850:669:GW1911032620th:6:1101:18304:1590 117 Scaffold23667 14021 0 *= 14021 0 TTCACTAGGGAGAATATAACTTTTGTTTAATTGTAGTTATATATAGTAGAAGATCTATTAAGCATGGATTTTATTATGTCCAGCTGTCAGAATTCACTTCTTTAATATAATTAATATTTTTTGTTTTACCAGAACTCATTCATCTAACAN<<-A--7--7<-FA----7-<--<F7A-7-7---7--J-F7-7-<--A-77-A<---7--7--7-7-A77--7-7-A-7--A7-FAA-A<<---<FAJF<JJF<--JJ<-F7<---7FJFJ<-F7AFAFA-A7F7<AJAA7-FAFA<AA# MC:Z:150M AS:i:0XS:i:0 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:18304:1590 185 Scaffold23667 14021 60 150M = 14021 0 TTCTTTTTAATGGATTTATTTTCGTAACAACATGGCCAATGTTAAGGTCATTGAAATCATTATGAGGACAAAATGTTTTTGATATTCATTATAATTATTATAAACAATAAATATTTGTGTGTGTGTGTCAATTATTGATGAAAAAAATTN JF<F-F<F<--7--AF<-JF<A-7A<-FA<7FJ7A---A7-7--7-7-7-<7-A<7-<FF7FFAF-<A-FA-A<77---7-FA-JA7<-FA-JJJJJJJ<<-<<<---JJF-A<FF-JAJFF7FJJJJJFJ<JFJFJJF-JJAFF-FAA# NM:i:17MD:Z:4C13A22A0C2T1G8A19G11G2G9T2A12C1A13G11T3G0 AS:i:70 XS:i:21 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:7050:1713 81 Scaffold2303 9825 60 24M4D126M = 9767 -212 CTTTGTTGTAATAAACATCTTGAGAATATTGATCAAATAATAAATAATAATAACGCATATATATATTATATATAAGTAAACAAATAAAATCTTGTTTACAGAATCACCTAATTTGTCATCAGTCACTTCAATACTCGAAAAGTACGTGTN J<----FAF<7-7-A<F<A--77--JFA-7--7-F<7-JA7FA-<FA7JA-JF<-7F7FFJJAFF7F7-JFF7AFFJJJJJJJF<JJFFAF<-FF<FF<F-FFJJJJJ-JF<-<AJJJJJJJAJJJFA7JAFAFFJAJJJFFFFFAAAA#NM:i:9 MD:Z:24^GCTC0C6T4T6T105A0 MC:Z:83M4D67M AS:i:119 XS:i:21 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:7050:1713 161 Scaffold2303 9767 60 83M4D67M = 9825 212 NGTCAAACCAAATATCTACTACAAAAAAAAAATAATCTCACAGTTTCAATGTATTCTGCTTTGTTGTAATAAACATCTTGAGGATATTGTTCAATTAATAATTAATAATAACGCATTTATATATTATATATAAGTAATCAAATTAAATTT #AAAAFFFAF<JJJJJA<-F-<<A--7F<FJJJJFJ-F<-FJFFJF<-<AFJ<7JAJJ-FFF7-AFJ-777-A--<-<A-77AAFJJFFJJ<-7AJJJF<-AA--A-77--7<7-7-7<F-A7AF-<7A--A--7<J-7-AA<-<-<<-< NM:i:9MD:Z:0A82^CTCC33A20A5A4C1 MC:Z:24M4D126M AS:i:122 XS:i:21 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:4137:1731 117 Scaffold39011 3930 0 *= 3930 0 GTTTTGAGAGACATCTCTCAACTATATGTTTTCAGCTCGATCCAGCAAATAACGTCATGATCAAGTTGCACGTGGGACACATAAACTGTGTAAACATGTATCCGAGGCCCTCATTGTAAAACCTGTGAACACTAGTTCGCGCGTGCGTAN---A7----<--A------7--77-AJA77----A7-A-777A-A-<7-AAFF7--<---<-7-----7-7--7----A7----A7-<A-F-A-F7---------7-----<-<---AA7-7FF<J--<F<F77<F-A7JJJFFFA<AA# MC:Z:5S79M66S AS:i:0XS:i:0 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:4137:1731 185 Scaffold39011 3930 60 5S79M66S = 3930 0 TATTAAAGGAAGCCCTCGCATATATGGTTATAGACTTTATGCGTCACACATATCAATTGCTTTTCTCGCTGGTTACAGGATCGATCTGAAAACATATATTTCTTTCATTAGTTGCAGTACAAGAAAAATTAGATATGCTTACTATTATTN 7-77-<-7-7)-)A)A-7---------F--<7-7--7--7--7-------7--F<A7A7-7-FA-AA--<--7A<---7<-FJAAA-<----JAJFJ<-<-<-A7---<----<--<-----JFA-7F--F7J-JAF<-FJFJJF-AA<# NM:i:6MD:Z:21T5C8T17A8T1A13 AS:i:49 XS:i:0 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:8156:1801 81 Scaffold13304 2184 60 74S76M = 2130 -130 GGGACTCGCCACAAATGATCTTCTACCACCACCATACACATTTCGTATATCGACTGCATAGCGCGGTCCAGGTGTTGTATAACAGTGTAGGAGCAAGAGACAGCTGTGCCCACGCACAGTTTTTTCCTCTCTCGTTCTCATAGCTAGTGC <))<))<--7---777----7---7A-777--7F7--7---7---7-<-77--77-7-<7--7-77----77--A-F-JF-AA<-7F-A-<7-AJA-A-<77---JFAA<7--<--JJF-F<-<7AF<-AAA-<7AA7JJFA7JFFAFAA NM:i:0MD:Z:76 MC:Z:90S60M AS:i:76 XS:i:54 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:8156:1801 161 Scaffold13304 2130 60 90S60M = 2184 130 NTCATGATAAGGGTAAAAGAACTAATGCAAATGGATGTTTTGATATATTTTTTCCATTGAATTGATTGTTGGGGGTCGCCGAAAATGATGTTCTCCCACCTCCATTTATGTTTCGTATATCTACGGCATAGCGAGGACTATGGTTTGTAT #AA<FJAFJJ7FFFJJFA-7-FFJ-<<J--<JJJFFA<A-JJA--<FA-<--<-<FJ<-<7<J-<AAAJJ-F-<--7AA-AA<JAFF-F-AJ-FJ-F-77-A<-77---7<J-A-A-7F-FFFA-<)))--A7A<)AF---7-7--<--7 NM:i:1MD:Z:10G49 MC:Z:74S76M AS:i:55 XS:i:25 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:14316:1854 77 * 0 0 * *0 0 GCATGTATGTTGCTATTGTTGTAGGGATCGTGACGCGATTCATGTTGCTGTGGACTACGTGTATTTATTTTTGTACTTGTCTTTTATGCTGATGTTGGAGTGCACGAGTTGAGAATGGGTATCGTATGTCGTCTTGGTGTTGGGATAATT <AAAAJ<AAJJ-AJ-AFAJJ777-FJ-7--<F----7-7--<<-<FA---<7-<--<-<<<<<-<7-AFFA--<---<A--<7---<--7--<77----7---7-7-7---77--77-7-----7--------7<----7-7-)----7A AS:i:0 XS:i:0 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:14316:1854 141 * 0 0 * *0 0 NTTTAACATTAATTTCACGTGTTTCTTTGCATTATGAATGTTGTCTGGATCGCTGTGTCGCGTGGAGCGTGCAGGCTTGTGTGTTTTACACGTTTGATGATTCCGGCGACTCGCGTCGTTTAGGTTTCGGTGGTAGCTGTGTTTTTATTT #AA<<A-A-A-A----A-<<A-<<F-FJF-7-<-<<--<--<<F---7-<--7<--7---7--7---7-77--7A-777F-<-<A-7-----<-7F7-7-7---7--77-7-7--F)-)-7---7-7--7<)-F-7--777--777---- AS:i:0 XS:i:0 RG:Z:a