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Missing coverage information after merge_linear_paths() #29

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jamiemcg opened this issue May 15, 2023 · 0 comments
Open

Missing coverage information after merge_linear_paths() #29

jamiemcg opened this issue May 15, 2023 · 0 comments

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@jamiemcg
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Is it possible to keep coverage/count information when using merge_linear_paths?

E.g., this is snippet of my starting graph which has FC tags:

S	35	TATTTTTATTAGAGACCTTGATTCCGATAATATTCATGTTGTATTAGCCGATTTTGGTCTAGCCAAAGCAAGTATGGGTTCAGTTGACAGATCCTATGCTGGCACTCCTTTATACATGTCTTTAGAACTCGCAACCGGAGGAAAGTACAGTTTCAATACCGATATCTATTCATTGGGAGTGGCTATCTATCAAATCATGACCAAAGACACAACCACAGCTGTCAGTCACATGTTTATTTCGAATAGAGAGGAAGAAGCAATTGATAAATTAACAAAGGAAATGGAAAAATCAGGAAATTATTCAACAACATTGATTAATATTTGTTTATCTATGCTGGAGAAGGATGCCAGTAAGAGACCAAGTGCCAAGCAAATCCTTTCCAATACTTTCTTGGAAGATATTCTCATCACACCAACAGAATAAACAATTTCTTGTGTTTTACCGCTGAAGTTAACCGTTAGAATTATAATAATTTTATTTTTCACAACAAAAAAAACAAGCCAACAACAATAGAGCGGGTGCAAACTCGGGTGTATCTACCGTTTTTCGTTTCTGAAAACGACTTTCGTTTTTGTTCGTGTTTGAATGAAGATTTTTGGTGTTTCTTTCAAATTCATACAAGATCGTTTTTCGTTTTTGTAAAAAGTTAGAAAAATACGAAAACGTGGCAAGTTGCACCTGCTCTAATGTGGGCAACAAACTTGAGGTTACCATTACCTTCTTGAATGATCATCAGAAGATTATTCATCTTCGCTTACCATCAGAGATCTGATTATTAACCGCTCTTGACTGTCAACTGAGATTTGGCAGGTGAAATTCAGTTTTCACATTCGCCAAAAGAAAATGAAGATAAATGATGATGAATTGAATAATTCTTGAATTTCTTCCTACGGATAGCTATGCATCATTCTCACATATCAATAGGCAGTGTCAATCTATTCTTGTTTCGGAAAAACCAAACTTTTGGAAACAGAAAAAGAGTGAATATGATAGAACTATTGCCAACCAAGAACGATACCTCGACCATGTTATTGATACAATGACAAGAAATGCTTCTAAGAACAATTATTGTTTATTTGCTTGTTTTGTCGGGATGTTGTTTTCGTTTCTTGTGTTTTTACCAGCATTTATGATCATGGTGATTATGGCATCTAGTTCCCTTTCAGGAAATATATTGAATTGTGAGAGGAATGTTTCTTCTATTCAAGTTTTGAATAGAACTATTGAAAGGGTTTCTTATCCAGGATGTGTAGAATGTAACACAATTTGGAATACTAGTTGCAATAATTTCAATGTTATGCCATGTTGTCAACCAAATAATAGTTATTCTTCAATTTTCTCATATGAATGCAATGTAACTGAATGCATTAAGGAAAATTATCAAGATGGACCTCTCAGATGTCGAGTAATTAGTTACAACAACAAAAAAGGGCCATCCACATATTCACTAGTCATTTACAAACCAGAAAGCAATTATTCAGGGTCTATAGGACTATTATCTGGTTAGCTACCAATACTTATGATTTGAAAGTTTAGTCAGATTACTGAAATACTGACTTTATTTCACTAACAACACGTAGGTCGGCAATGTGATTCCTTCTTCATAATTGAGTATTAATCGTACGGTATTTGCAAGTAAATAATAACTAATAATGGTCAATTAACAAAATATTAAATAAATTATTTAAAAAAAATGAAAAGAAGCAGAGAGGAGGAACCTGCTGTTACCAATACATCATGTACTGATCAAAGTAATACAAGTTCCGATCCTCTCTTGGAAACGAATCTAAAAAAACAAGTGACTGGCAATATTT	ll:f:44.5	FC:i:80768	kl:f:44.5
S	11508	ACTGTCAACTGAGATTTGGCAGGTGAAATTCAGTTTTCACATTCGCCAAAAGAAAATGAAGATAAATGATGATGAATTGAATAATTCTTGAATTTCTTCCTACGGATAGCTATGCATCATTCTCACATATCAATAGGCAGTGTCAATCTATTCTTGTTTCGGAAAAACCAAACTTTTGGAAACAGAAAAAGAGTGAATATGATAGAACTATTGCCAACCAAGAACGATACCTCGACCATGTTATTGATACAATGACAAGAAATGCTTCTAAGAACAATTATTGTTTATTTGCTTGTTTTGTCGGGATGTTGTTTTCGTTTCTTGTGTTTTTACCAGCATTTATGATCATGGTGATTATGGCATCTAGTTCCCTTTCAGGAAATATATTGAATTGTGAGAGGAATGTTTCTTCTATTCAAGTTTTGAATAGAACTATTGAAAGGGTTTCTTATCCAGGATGTGTAGAATGTAACACAATTTGGAATACTAGTTGCAATAATTTCAATGTTATGCCATGTTGTCAACCAAATAATAGTTATTCTTCAATTTTCTCATATGAATGCAATGTAACTGAATGCATTAAGGAAAATTATCAAGATGGACCTCTCAGATGTCGAGTAATTAGTTACAACAACAAAAAAGGGCCATCCACATATTCACTAGTCATTTACAAACCAGAAAGCAATTATTCAGGGTCTATAGGACTATTATCTGGTTAGCTACCAATACTTATGATTTGAAAGTTTAGTCAGATTACTGAAATACTGACTTTATTTCACTAACAACACGTAGGTCGGCAATGTGATTCCTTCTTCATAATTGAGTATTAATCGTACGGTATTTGCAAGTAAATAATAACTAATAATGGTCAATTAACAAAATATTAAATAAATTATTTAAAAAAAATGAAAAGAAGCAGAGAGGAGGAACCTGCTGTTACCAATACATCATGTACTGATCAAAGTAATACAAGTTCCGATCCTCTCTTGGAAACGAATCTAAAAAAACAAGTGACTGGCAATATTTCTAGTGAATCATCGTATTTTAGTCTTGGTTGTAATTATATGGATGGTGTTAATGGTGTTGAAAAAGATTATTTAAAAGCATTTGAATTATTTTCTAAAGGTGTTGAGGAGGGATGCTTGCGATCAATACATAAAATTGGTTACTTTTATAGCAAAGGATTGGGAGTTGAACAAGATTATGATAAAGCAGTCCAGTTCTATATGAAATCTGCTGAAGGGGGTTTTGTGGCCTCATATGCTAAGGGAAAGGCGTTCAACAGGACCATGTTAAAGCATTTGAATGGACTTTAAAAGCTGCTGAAAATGATAATACTGATGCACAATTTAACATTGGAAGATGCTATAGTAAAGGGACAGGAGTTGAGCAAGACCATGTTAAAGCATTTGAATGGTATTTAAAAGCTGCTGAAAAGGGTGATACAGATGCACAGTTTGTGATTGGA	ll:f:43	FC:i:63124	kl:f:43

But when I run graph.merge_linear_paths() the FC tag is lost:

S	35_11508	TATTTTTATTAGAGACCTTGATTCCGATAATATTCATGTTGTATTAGCCGATTTTGGTCTAGCCAAAGCAAGTATGGGTTCAGTTGACAGATCCTATGCTGGCACTCCTTTATACATGTCTTTAGAACTCGCAACCGGAGGAAAGTACAGTTTCAATACCGATATCTATTCATTGGGAGTGGCTATCTATCAAATCATGACCAAAGACACAACCACAGCTGTCAGTCACATGTTTATTTCGAATAGAGAGGAAGAAGCAATTGATAAATTAACAAAGGAAATGGAAAAATCAGGAAATTATTCAACAACATTGATTAATATTTGTTTATCTATGCTGGAGAAGGATGCCAGTAAGAGACCAAGTGCCAAGCAAATCCTTTCCAATACTTTCTTGGAAGATATTCTCATCACACCAACAGAATAAACAATTTCTTGTGTTTTACCGCTGAAGTTAACCGTTAGAATTATAATAATTTTATTTTTCACAACAAAAAAAACAAGCCAACAACAATAGAGCGGGTGCAAACTCGGGTGTATCTACCGTTTTTCGTTTCTGAAAACGACTTTCGTTTTTGTTCGTGTTTGAATGAAGATTTTTGGTGTTTCTTTCAAATTCATACAAGATCGTTTTTCGTTTTTGTAAAAAGTTAGAAAAATACGAAAACGTGGCAAGTTGCACCTGCTCTAATGTGGGCAACAAACTTGAGGTTACCATTACCTTCTTGAATGATCATCAGAAGATTATTCATCTTCGCTTACCATCAGAGATCTGATTATTAACCGCTCTTGACTGTCAACTGAGATTTGGCAGGTGAAATTCAGTTTTCACATTCGCCAAAAGAAAATGAAGATAAATGATGATGAATTGAATAATTCTTGAATTTCTTCCTACGGATAGCTATGCATCATTCTCACATATCAATAGGCAGTGTCAATCTATTCTTGTTTCGGAAAAACCAAACTTTTGGAAACAGAAAAAGAGTGAATATGATAGAACTATTGCCAACCAAGAACGATACCTCGACCATGTTATTGATACAATGACAAGAAATGCTTCTAAGAACAATTATTGTTTATTTGCTTGTTTTGTCGGGATGTTGTTTTCGTTTCTTGTGTTTTTACCAGCATTTATGATCATGGTGATTATGGCATCTAGTTCCCTTTCAGGAAATATATTGAATTGTGAGAGGAATGTTTCTTCTATTCAAGTTTTGAATAGAACTATTGAAAGGGTTTCTTATCCAGGATGTGTAGAATGTAACACAATTTGGAATACTAGTTGCAATAATTTCAATGTTATGCCATGTTGTCAACCAAATAATAGTTATTCTTCAATTTTCTCATATGAATGCAATGTAACTGAATGCATTAAGGAAAATTATCAAGATGGACCTCTCAGATGTCGAGTAATTAGTTACAACAACAAAAAAGGGCCATCCACATATTCACTAGTCATTTACAAACCAGAAAGCAATTATTCAGGGTCTATAGGACTATTATCTGGTTAGCTACCAATACTTATGATTTGAAAGTTTAGTCAGATTACTGAAATACTGACTTTATTTCACTAACAACACGTAGGTCGGCAATGTGATTCCTTCTTCATAATTGAGTATTAATCGTACGGTATTTGCAAGTAAATAATAACTAATAATGGTCAATTAACAAAATATTAAATAAATTATTTAAAAAAAATGAAAAGAAGCAGAGAGGAGGAACCTGCTGTTACCAATACATCATGTACTGATCAAAGTAATACAAGTTCCGATCCTCTCTTGGAAACGAATCTAAAAAAACAAGTGACTGGCAATATTTCTAGTGAATCATCGTATTTTAGTCTTGGTTGTAATTATATGGATGGTGTTAATGGTGTTGAAAAAGATTATTTAAAAGCATTTGAATTATTTTCTAAAGGTGTTGAGGAGGGATGCTTGCGATCAATACATAAAATTGGTTACTTTTATAGCAAAGGATTGGGAGTTGAACAAGATTATGATAAAGCAGTCCAGTTCTATATGAAATCTGCTGAAGGGGGTTTTGTGGCCTCATATGCTAAGGGAAAGGCGTTCAACAGGACCATGTTAAAGCATTTGAATGGACTTTAAAAGCTGCTGAAAATGATAATACTGATGCACAATTTAACATTGGAAGATGCTATAGTAAAGGGACAGGAGTTGAGCAAGACCATGTTAAAGCATTTGAATGGTATTTAAAAGCTGCTGAAAAGGGTGATACAGATGCACAGTTTGTGATTGGA	ll:f:44.5	kl:f:44.5	LN:i:2257
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