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mengyao / Complete-Striped-Smith-Waterman-Library

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SEQ and QUAL have different lengths #42

Closed sdwfrost closed 2 years ago

sdwfrost commented 7 years ago

I can't process the SAM output from ssw_test with samtools as the sequence length and quality score are different lengths:

ssw_test -m 1 -x 2 -o 4 -e 3 -f 14 -r -s -h -c ref.fas query.fastq > query.sam

followed by

samtools view -bS query.sam

gives

[E::sam_parse1] SEQ and QUAL are of different length
[W::sam_read1] parse error at line 3
[bam_flagstat_core] Truncated file? Continue anyway.

The first line of my SAM file is:

@HD VN:1.4  SO:queryname
@SQ SN:EU239217.1   LN:3212
NS500125:171:H5WMJAFXX:4:21605:21022:14089  16  EU239217.1  2682    5   104S14=32S  *   0   0   TTGTATTGAAAAACTCACTTAGATTTTATATTTTGTTATATTCTAAAAGTTTTATGGTTTTTCATTTTGCATTTGTGTGTATGATTCATTTTGAGTTCATTTTTGAGAAAGGTATAAAGTCTGTGCCTGGATTAATTTTTTTTTTTTTTT  /E<EE<EEEE/<EE  AS:i:14 NM:i:150    ZS:i:10

The quality string is way shorter than the sequence.

mengyao commented 7 years ago

Dear Simon,

I apologize for the error.

It has been fixed. Please clone and try the latest version.

Please let me know, if you find any other problem.

Many thanks,

Mengyao

On Fri, Nov 18, 2016 at 10:08 AM, Simon Frost notifications@github.com wrote:

I can't process the SAM output from ssw_test with samtools as the sequence length and quality score are different lengths:

ssw_test -m 1 -x 2 -o 4 -e 3 -f 14 -r -s -h -c ref.fas query.fastq > query.sam

followed by

samtools view -bS query.sam

gives

[E::sam_parse1] SEQ and QUAL are of different length [W::sam_read1] parse error at line 3 [bam_flagstat_core] Truncated file? Continue anyway.

The first line of my SAM file is:

@HD VN:1.4 SO:queryname @SQ SN:EU239217.1 LN:3212 NS500125:171:H5WMJAFXX:4:21605:21022:14089 16 EU239217.1 2682 5 104S14=32S * 0 0 TTGTATTGAAAAACTCACTTAGATTTTATATTTTGTTATATTCTAAAAGTTTTATGGTTTTTCATTTTGCATTTGTGTGTATGATTCATTTTGAGTTCATTTTTGAGAAAGGTATAAAGTCTGTGCCTGGATTAATTTTTTTTTTTTTTT /E<EE<EEEE/<EE AS:i:14 NM:i:150 ZS:i:10

The quality string is way shorter than the sequence.

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sdwfrost commented 7 years ago

Almost! It appears that the quality score is one base shorter than the sequence.

mengyao commented 7 years ago

I just made a update. Please have a check.

Sorry for the error.

On Sat, Nov 19, 2016 at 4:32 AM, Simon Frost notifications@github.com wrote:

Almost! It appears that the quality score is one base shorter than the sequence.

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