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Avoid truncating read name #3

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PeteHaitch
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Issue: Read names are truncated by trimadap-mt when the read name contains whitespace
Fix: Use KS_SEP_LINE rather than KS_SEP_SPACE

I hope this is correct way to fix this issue.

Example data

$ fastq-dump -X 1 --readids -Z SRR891268
Read 1 spots for SRR891268
Written 1 spots for SRR891268
@SRR891268.1 HWI-ST281:266:C1LTTACXX:1:1101:1238:1978 length=100
NTCGGGAGGATCCTATTGGTGCGGGGGCTTTGTATGATTATGGGCGTTGAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAAT
+SRR891268.1 HWI-ST281:266:C1LTTACXX:1:1101:1238:1978 length=100
#1:BDD?DH<AAFF@GGGIEHACFHII?DFEEE;@D6@C>ACDD(8?BD#11:ABDEA==CFFBBBBCCA?ECEFI?::CC?CBGBFDGHIJJGHGIHHG

Current behaviour

Read name is truncated on line 1

$ fastq-dump -X 1 --readids -Z SRR891268 | trimadap-mt
Read 1 spots for SRR891268
Written 1 spots for SRR891268
@SRR891268.1
NTCGGGAGGATCCTATTGGTGCGGGGGCTTTGTATGATTATGGGCGTTGAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAAT
+
#1:BDD?DH<AAFF@GGGIEHACFHII?DFEEE;@D6@C>ACDD(8?BD#11:ABDEA==CFFBBBBCCA?ECEFI?::CC?CBGBFDGHIJJGHGIHHG
0               AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
0               AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
0               AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
0               ATCTCGTATGCCGTCTTCTGCTTG

Patch behaviour

Full read name returned on line 1

$ fastq-dump -X 1 --readids -Z SRR891268 | trimadap-mt
Read 1 spots for SRR891268
Written 1 spots for SRR891268
@SRR891268.1 HWI-ST281:266:C1LTTACXX:1:1101:1238:1978 length=100
NTCGGGAGGATCCTATTGGTGCGGGGGCTTTGTATGATTATGGGCGTTGAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAAT
+
#1:BDD?DH<AAFF@GGGIEHACFHII?DFEEE;@D6@C>ACDD(8?BD#11:ABDEA==CFFBBBBCCA?ECEFI?::CC?CBGBFDGHIJJGHGIHHG
0               AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
0               AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
0               AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
0               ATCTCGTATGCCGTCTTCTGCTTG

…tured and not truncated (e.g., if it contains a space)
@lh3
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lh3 commented Feb 11, 2017

Via ddfef21.

@lh3 lh3 closed this Feb 11, 2017
@PeteHaitch
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Thanks, Heng!

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2 participants