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Fix to seqindex.cpp to allow tabs in header line #28

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Sep 13, 2024
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@lcoombe lcoombe commented Sep 11, 2024

  • It was reported in Unable to run simulated human HiFi reads goldrush#138 that goldpolish was throwing an error when inputing reads that had tabs separating the id and other information in the header
  • The current code handled spaces after the id, but not tabs
  • To fix, do another split of the ID in seqindex.cpp by tab characters to account for this
  • The test reads file was updated to include reads that space-separated and tab-separated comments in the header line:
(btl) [lcoombe@hpce705 test]$ cat test_reads.fq |sed -n '1~4p' |head -n3
@SRR10028109.589610	st:Z:2024-03-14T09:22:04.350+00:00      RG:Z:ccf17720be1a9a9f8f33443ea90c42b6a7685e7f_dna_r10.4.1_e8.2_400bps_hac@v5.0.0
@SRR10028109.366284 st:Z:2024-03-14T09:22:04.350+00:00	RG:Z:ccf17720be1a9a9f8f33443ea90c42b6a7685e7f_dna_r10.4.1_e8.2_400bps_hac@v5.0.0 test
@SRR10028109.540860

@lcoombe lcoombe requested a review from jwcodee September 11, 2024 22:45
@lcoombe lcoombe merged commit 7051db4 into master Sep 13, 2024
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@lcoombe lcoombe deleted the tab_fix branch September 13, 2024 18:47
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2 participants