bridge_lchains assertion error #78
Description
Hi,
With the prebuilt GRCh38 pangenome graph I am getting an assertion error.
minigraph -t 1 -cx lr GRCh38-90c.r518.gfa.gz reads.fa
minigraph: gchain1.c:391: bridge_lchains: Assertion l0->v == l1->v' failed.`
Below is a single read that reproduces the error:
>read
TACTTCGTTCAGTTACGTATTACTAGTTTCACCCACGCTTTGCTGACTGACCAACACACTGAAGCTCCCTTCAAACCCAGAACTTACTGCACTTGCTTCTAAGATGCACCTGAAATTGCTGTTAGAAAAATGAAGCAGAGAAGGAGCTGCACGTGTGGGGGAGGTGAGGGTGAGAAGGAAGGAAAGGCACAATCTGTCACAGTTTCCAAACACATATGCTTCGCGTGGGAATCTGGGGTTGATTCAAAGGCTGAATGGATCTTCAGTTACTGGAAGGCTTGGCCCAAAATATTTCAGTATATGGAGCAGTTCTCTTCCTTCTAGTAGCAAAAGCAGCAACTGAGAGTGACTGGATTTGTGATCCAGAATGGGGACAGTGGGAAAAGTGCAAACCAATTCTCAATGGAGAAAATAGCCAACTGGTCAAGGAACTGTGATGAGATGGCGGGATTCTCCAGGAGGTGCGTGATGTGGCTGAGGTGCCCATCCATCCTGTATGATGATGACCAAACTCGTCCAGGAGCGAGATGTGGCCGGTGCCCATCCATCACTTGAAAACATGATGGTAAACTCGTCAGGAAGTGTGTGATGTGGCCGGTGCCATCCATCCTGTATGACGGTGAACTTGTCCAGGAGCGAGATGTGGCTGGTGCCCATCCATCCCATATGATGTCCAAACTCGTTCAGGAAGTATGCGGCCAGCGCCACATCCATCTGTATGATGGTGAACTTATCCAGGAGCGAGATGTGGCCGGTGCTTACATCTATCCCATATGATTGTAAACTCGTCCAGGAAGTGTGTGATGTGGCCGGTGCCCATCCATCTGTATGACGGTGAACTCGTCCAGGGCAGAGATGTGGCTGGTGCCCATCCATCTCCATATGATGGTAAACTCGTCAGGAAGTGTGTGACGTGGGGAGCGCCCATCCATCCTGTATGATGGTGAACTTGTCCAGGAGCGAGATGTGGCCGGTGCCCATCCATCCCATATGATGGTAAACTCGTCCAGGAAGGTATGCGACGTGGCCCGGCGCCCATCCATCCTGTATGACGGTGAATTTGTCCAGGAGCGAGATGGCCGGTGCCCATCTATCCCATATGATTGTAAACTCGTTCAGGAAGTGTGTGACGTGGCCAGGCCACATCCATCCTGTATGATGGTAAACTTGATGGAGCATAGTTCCGGGAGCAGCTCTCCTGGGTTTAGGAAGTGGGGAGGGTGTGGGGGGTCACAGCCGTTAGTATGATGATCTTATCCGCTGCTTCAATTTCCTTCAGATAAATTTCAATATTTTTGCATTTCTTCTGGTCACAACTCTCATCCATGGACATTTTAGAGGTAACAAGCCCGCTCACATTTCCATAAATCAACATTGTGGCTTTCTGAGTCCGAATCGGACAGGACGTGGGCAGCTGGCGCTGTTGGTCTCCACTCTCACTGGGCTGAGGCGCACTGAACCCAGAAACCAACACTGCATCGCTACAGATTCTCTCTGACCTGGTGCCGAAAGGGCTTCAGCGGATTTCTCCTCTGCCAACGTCCTTCGAAACTCTCTGTAGTACTTTCTATCCGCCAATCAATGAGCCAGCCAGCACATTCCCTGTGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGTGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCTGTGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGAGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGTGATCAATCCATCAATTCCACCCACCAGTGAGCCAGCAGCACTCCCTGTGATCAATCAAGAAGCTCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGTGATCAATCCATCAATTCCACCCACCAATCGTGAGCCAGCAGCACTCCCTGTGATCAATCCATCAATTCCACCCACCAATCAGTGAGCCAGCAGCACTCCCTGTGATCAATCATCAATTCCACCCACCAATCAGTGAGCCAGAAGCACTCTGTGATCAATCCATCAATTGATCAGTCGACCCACCCGCTGGCTACCAGGGGCACCCAGCGCAGCTGCGCTCACAGAGTCAGGGCGGCGGCTCAGACAGAAACGTGGGTGTGCTTGTGTGTGCAGAGTGCACGCTGCAGAGAAACCACGGGGCTGCAGGCCCAGCCTCCAGTAGAGCCTGGAGCCGGCCTGCAGGGAGGACCCCAGGCGGGTGTGGGGACCCACCTTAGGAGGACAGACGCACATGAGGCTACGGGAAACTGTTGTCATGAACCCCAAATGTGTTGTCAATAAGAGCACCGGACTTAACTTTCAATGCTTCTCTTAGCAAAACCAGGGATTTTCCTGCAGCTGCATGAACATTGACCTGTCCGCCTACTCCCGAGCCACAGATCTGGGGAAAGAATGCATGTAGCCTGCTGTGGGTGAATGGAGCTGGGGCAGTGATGAGCTACTTCTTGCCTTTTGTCAGGGGAAAAGGAAGCTGGATAGATTTCTCTTCTCTTCCTTTGAGAATGAGTGAAGAGGGAAGATAAAAGCCAGCAACCAGGGACAGCTGAAAATATGGTTTCAGTAAGAGACAGGCCACAGCGTCTAGGCCCCTAGGACAAGCAGACCTTCCAGGAGGATTTCTAAGGTGGCTGGAGAGAACTCTGCTACCCTTTCCAACAGATGCAAGACACAGCCTCTCTAAAAACAGGAGCAGAAACACACAACACGGAAAAAACAGGGTGTCAGCTGAACCGTTACCAAGTTATGAGCAAAGAGGCTGGAACTGGGAGAGATGAGAAATAACTGTGAGGAAATTAAAACTACAATAGCAGAGTTAAAATTCACATTGAGGCGGCAGAGCAGAACTGACTACAGTTCACAACCGAACCATAAAGCTCTCTTCGAGAATCACGGAAACAAGCACAAAAGATGCTAAAAGAGGGATATTAGAGACGTACGGCACAGGAAAGAGAGACTCGTCCTAAGGATGGGAGAGTTTGGAGAAGAAGCTAGAATGACTAGTAGGAAGAACAGGAAACAGGGATCTGCAGCAATGCCTCGGCTCTCAGGGGGCGCTCAGGGAGGTGCAGGGCAGAAATTAACAACATAGCCGAAGAGGGTGCACTGCAAATGCGTGGAAACAATGGCTTATTCAAGAAACTAGAGTTTACTTGGGGAAGGTCCTAGTTTATCCCTCACTTCACACACATTACAACCACCAGAAATGATCCAGATACATTAACACATTAATGGAACCATAAAAATAACAAATAAAAACTTGTGTTTCACTGATGACAGGATGAGCAAGCACTTTCTAAACATGAGAGCGATTGACAAAATCTTAAAGGAAACGACTGTGCATTTGAATCCACCAGAGCTCAGCCTTTCTGAACTTCAGACAGTACAACAAGCAACGTTAGACACAGACAAGCCTGGCAGAACATTGGCCAAAAGTAAGAGGCAAAAAACAAATATGAAGAAGTACTCGTGAGTCTATTTCAGAGAATTCACACTCCCATAGGAAAGATTCATGAAGAGATTATCCCAGGAAGCAAGACATCAATAATCAAGTATGATAAAATGTTTAAATCTACAATAAATCAAAAACTATAAATTAAACCAATGATAAGATGCTGTCGTTTGCCCTAAATAATTGCATACACTTGACTGAAGTCCTAACCTGGAGTGGCTAAGTGTGATGGATGATGTGAGTTCATGGACTTGCCAGATGCTTATATTTGTTTGATGTTCACATTCATGGATAAGGAATTGAGGTATTTAGAAGAGCTTGCACCATTTCACATAGTAGTTAGATTTCTAGGAGTGTATCCTAAAAACAGTAAGCCACATAGATTGAATGTAGGATATTAATTGCAGCAAGACTTATGATAATGAAATACTAGAAACAAGCTAAATGTTCAACAATAGCACATGGAGTTGAAAAACTTACAGCAGAACCACATAAAGACCAAAGTGTTCCTCAGAAGCATATTTTAAAGACAATTTGATAGAACACATAGGCAATAAGAATAAAGACACACATACATACACACATATACACATCCTAAAAGAATATCAGAATAGTAAGCATTTTCCTGAGTTTTCCACTAAGTCACTGAACTGAAACAAGTATTTGCTTTTAAATAGATTTCTGAATTAATATAGAGAGGTTTATTTCTGTCTTTGATACTGTGTCTGGCCTGGACCATTTTTAATTGCTCAGAGACTTCTAGGTGTGTCATAAATCTCTGTACAACCAATCATTCATCCATCCATCCATCCATCCATCCCCCGACCAAACCCACCCACTTACTCATCCATCTGCCACCCACCTGCCTCTACCACCTATCCTCACCTGCCTGTCCACTCACACCACCTGTCCATCTACCCTTCCATGCATCCCTCCATCCACCCACCCATCCACCCACCACCTGTCCACCCACCCACCCATCCACATCTGCCTTTCCATGTCCCTCCACCCATCCACCCACCCATCCACTCACCACCACCTGTCCACCTGCCTGCCCATCCACCCGTCCACCCTTCCCATGTGTCCCTCCACCCACCCACCCATCCACTCACCACCACCTGTCCACCTGCCCACCCATCCACGCATCTGCCCTTCCATGTGTCCCTCCATCCACCACCCATCCACCCACCTATCCACTCACCACCACCTGTCCACCTGCCCACCCATCCACACATCCGCCCTTCCATGTGTCCCTCCATCTCCACCCCATCCACCCACACCACCTGTCCACCCGCCCACCCATCCACACATCCCGCCCTTCCATGTGTCCCTCCACCCATCCACCCACCCATCCACTCACCACCACCTGTCCACCTGCCCACCCATCCACACATCCCGCCCTTCCGTGTGTCCCTCCACCATCCCACCCACCCATCCACCCACCCATCCACTCACTACCACCTGTCCACCTGCCCACCCATCCACACATCCACCCCTTCCATGTGTCCCTCCACCCATCCACCACCCATCCACTCACCACCACCTGTCCACCCACCTGCCCATCGGCACGTCTCCATCTACCCACCCACCCAGAGAATTGCTCGCTTGTTGTGTGCTGTGGGCCAGGCTCTGAGGTTTATGGACGGCTGGGACATTATTAATGCCCATGGGGGATGTAGTGTCTGATGGAAGAGGTGGTGGAGAGGAGAACTGTTTTGATGCAAGTCCATCCGAGATGGCTCAGAAGGGCACCATGAGAGCCAGGGCCATGTACCACATTCTGTGGAGGTCGACTCCCCAGCACACGCACCCAGGAACACCCTGGGCTTGACAGCCATCTGCTGGGTCATGCCCTCTTGCTCTGTGCCTGAGTCCTTCGCACTCCTGCCGTCTGCAAGGACACGTCCAGCCCCCGCAGGGCTGGGGACTCCCAGCCTCCTCCATGACCCTCACAAGGACACAGTGTAGCCCAGCCTCCTGCAGGGCAGGACTCACATCCTCCTTCACTCCATGACCCTTCCTTGTTGCCGCCACACGTCTGTTGCACCTGTAGACACGGAGCCTTGGACTCAGGGGTGGGTCCCGTGGATCTCACAGCCCTGCTGCCCAGCATAGGACACTTTGCGTGTCAGTGAGTCCTGCTGAGTGGATGGCAAGGAGAAAGCTCCTCTCCACCGTGGCTACTCCAGTTCCTCTCCCCGCAGTGGATGGCACGGAGAAACTCCCTCTCCACTATGCCTACTCCAGTTCCTCTCGTAGTGGATGGCTGCAGGAGAAAGCTCCTCTCCGCCGTGCCCTACTCCAGTTCCTCTCATAGTGGATGGTACGGGAGAAAGCTCCTCTCCACTATGCCTACTCCAGTTCCTCTCATAGTGGATGGCACGGGAGAAAGCTCCTCTCCACTATGCCTACTCCAGTTCCTCCTCATAGTGGATGGTACGGAGAAAGCTCCTCTCCATATGCCTACTCCAGTTCCTCTCATAGTGGATGGCCTTGAGAGAAAGCTCTCTCCACGCCGTGCACTATTCCAGTTCTCTCGTAGTGGATGGCATGGGAGAAAGCTCCTCTCCGCCGTGCCTACTCACGATTCTCTCGTAGTGGATGGCATGGGAGAAAGCTGCTCTCTGCCGTGTACTCCAGTTCCTCTGAGTGGATGGCACGGGAGAAAGCTCCTCTCCCCACCGTGGCCTCGGATTCCTCTCATAGTGGATGGCACGGGAGAAAGCTCCTCTCCACCGTCGCTGCTCCAGTTCCTCTCATAGTGGATGGCACAGGAAGAAGCTCTCTCCACCGTGGCTACTCCAGTTCCTCTCATAGTGGATGGCTGGCATGGAGAAAGCTCTCTCCACCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAAAACTCCTCTCCGCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAGAAAACTCCTCTCCGCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAGAAGCTCCTCTCCGCCGTGGCTGCTCTCAGTTCCTCACCGACAGTAGTGGATGGCACGGGGAGAAGCTCCTCTCCGCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAGAAAGCTCCTCTCCATGTGCTTCTCCAGTTCCTCTCGTAGTGGATGGCACGGGAGAAAGCTCCTCCACTGTGGCTACTCAGTTCCTCTCGTAGTGGATGGCATGGGAGAAAGCTCCTCTCCACCCCCGTGGCTACTCCAGTTCCTCTCGTAGTGGATGGCACGGGAAAACTCCCTCTCCGCCGTGGCACTCCGGATTCCTCTAAATGCCTTCCTGAGGTGGCTGGTGTTCTTGTCTTCGTGAAGTTGCCTCTGATTCCATCCTCTAAAAGCCAATGACTTATATTTGGCACAAGACAGATTAACACGTAATTGTTCTTTGCTGAATTGGTATCTGACTGTGTGAGTTGACTGACATGTATAGTCGTATGTGTATCTGAGTGTGTTTGAATGTATGTGCATGACTGTGAGTGCATGTTCATCACTGTCGGTGTGTCACTGTGTCCATATGTGTGGCTGCATGTGAGTGTATGACTGTGTGTCTGTGTGGCTGTGGGAGTGTATGTGGTGGAAGGTGTGTGTGGCGTGTGTTTGTGTTTGTGAGAGAGAGACTGTGTGTGTGTCTGGCTGTGTGTGTGGTTGTGTGACTGTGTGGGAGTGTATGTGAATGTGCATGTGGCTGTGTCTATGTGTCTGTGTCTGTGTGTGTGACTTTGTATTACTCTGTGTGTCTGTGTGTGTGTGTGGGGGTGTGTGTGTGACTGTGTGAGCATGTGGCTATGTGGAGTGCAAGGGCCTGTGTGGGAATGTGTCTGTGTATGACTGTGTGGCTATGTGTAGTGTGTGTGACTGTGTGTGGAATGTGTATGTGCAACTGTGTGGGAGTGCATATTCTGTGTGACTGTGTGACTGTGTGGCTATGTGAAGTGTGTGTGGCTGTGTGTGTGTATGTAACCATGTGTGGCTGTGTGGCCATATGTGACTGTGTGACCAGGTGTGACTGTGTGGCCACGTGTGACTGTGTGACTGTGTGTGACTGTGTGACCGTGTGGAGTGTGTGTGACTGTGTAACCATGTGGTGACTGTGTGGCCATATGTGACTGTGTGACTGTGTGTGACTGCGTGTGACTGTGTACGTGTGACTGTGTGACCACATTTGACTGTGTGGCCGTGTGTGACTGTGTGTGACTGTGTGACTGTGTGTGACTGTGTGACCACATGGAGTGTGTGTGACTGTGTAACTATGTGGAGGTGTGTGGCCATATGTGACTGTGTGACCGCGTGACTGTGTGACTGTGACTGTGTGGCCGTCACTGTTACCACATGTGACTGTGTGGCCCTGTGTGACTGTGTGACCGTGTGTGACTGTGACCGCGTGTGACTGTGTGGCCACGTGTGACTGTGTGACTGTGTGTGACTGTGTAACCGCGTGTGACTGTGTGGCGCGTGTGACTGTGTGACCGTGTGACTGTGTGACTGTGTGGCCACGTGTGACTGTGTGTGACCGCGTGTGACGTGTGGCCGCGTGTGAGCTGTGTGGCCGCGTGTGACTGTGTGACCGCGTGTGACTGTGTGACCGTGTGTGACTGTGTGACTGTGTGTGACTGTGTGACCGCGTGTGACTGTGTGACCGCGTGCGTGTGTGGCCACGTGTGACTGTGTGACTGTGTGACTGTGTGGAGTGGTGTGTGACTGTGTAACCATGTCCAGGCAGGGTGTAGGTGGAGAGGGTACGGGACGGGAGCTGCAGACAACATCCGAGCCGGCTGAAGCCAGAGCAGGCCCCGTGTTGGGGGTGGAGCCCCAGGGTGGTGCTGGATTCTGGACAGTGGATGACCGATGCTGACGCTGGCACCTGATCACTCCTACAGCCGCCACCAGGCAGCATCCAGAGCCCTCAGCGTTTTCACCCCGAGTGGGTTGCTGCTGTACTCAGCAGTCAGGGGGACAGGTTGTTTCTTCCTGAGGTCTCCAGGCCACACAGGACCCTGAGAGGAGCCCCGTCCTCAGACCCCTCCAGGAGCCAGAAGTGTTTCTTCTTGGAGAGGTGAGGGGCTGGGGCGCCCTCTCAGGCAGTGCAGGAGAAGCACCGGCGGGGGCTGGAGCCACACCTCACCGCCTGCCTGCCCCTCCTCCTCAGCGTCCTGCAGGGCAACCTGCAGATTCACAGCAGCCGCTGCCTGGCCTGGGAGCTCTGCAGTGCCTTCTGCTGGAAGTGCCAGCCGTGTCCGCCCTGCACTCGCTCCCAGCACAGGGCAGAGGCGGTCGCAGAGCTGCATGATCTACTTTAAGTTCTGTGAAAGTCCTTCTGCAGTAACAGTTCATGCGCTGGCCACGATGGCAGCAAGGGCAGCTTTAAGTTAATTCAGGCTGTTTGGAACAGGCTATGGGGTCTTAAGCTTCTTCACCCGCCTTCACTCCCCACACGCTCCCTGTCACTGGCTGAACATCGGTGAAGAGACCAAAACTGTGAACGAGGACATTATCCTAAAGTGCAGAGCCCCACATGGTGGGAAGAGCTCAAATGCTCACCTAACAGGTCGGCCTTCCTTTTCCACAAGTGGTTTTTCAAACTTACCCGTGGTGTACGTGGCTTTAAGTGAAACTTGGTGAAGGATCCTCCCCCTTCCCCACCCCACCCATGGTGATGATTTTGAAAAGCTCCCCCAAGGAACCCTAAATTAGTCTTAAACACACACACAAATCTATCTGAGGCAGGGAAGCTGCCCATTAAGGGCCAGTAATTACCCGAGGCTGCTGGGGTGCCTGCCTGGAAGGGCCCCACCACGGGGCCTTTATTGCTTCCTGGCCTGGCGGACTCTGAGGCTCATGCATTATTCAGGAGCACGTGGGACAATAAGGAAAGCCTTCATAGAAAGAAGCAAAGCTGGGGGTAAATAAAGGTTGTGAGAAACACTACTATTTTCTACATTTATGAAAATATTGCAGCGTTCAGGGTGCTGAGGACGTCCTCTCTGGTTATCAGGAGAACACCTGGATTCTGCGCTTTCCTTCCTGCGGGCCTGCAGCCTGCAGAGGCCCTGAGACAGCATACAGTACCCCGGGACTGTGTCTTTTTCCTCCTCCTCTCCCTTTCTCTCCCCTTAATGCAAAGCTTTGTCAAGCTAATACTTTAAAGCAATACGCTTAA
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Best, Tobias