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From http://www.bioinformatics.babraham.ac.uk/projects/bismark/RELEASE_NOTES.txt:
> Changed the FLAG values of paired-end alignments to the CTOT or CTOB strands so that reads can
> be properly displa…
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If the goformation project is never updated - squals should still be able to handle updating schemas...
which means dealing with enums, and readability - albeit the bar for that is set low enough t…
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The specifications for tabix and csi are incomplete, currently being variously only essentially a struct layout with no semantic explanation or restrictions, or a description of the underlying storage…
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I mapped a fasta (instead of fastq), so holding no quality score in there. Sam specs demand the QUAL field to have the same length as the SEQ field, or to be a '*'. In slamdunk dunk it seams that a ba…
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An alignment tool I use [BioKanga](https://github.com/csiro-crop-informatics/biokanga) does not NUL-terminate the header in its BAM output files. According to the spec, it is valid that the header doe…
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Hi,
I wonder why `-` are not allowed in my reference. I had to use `_` to overcome this.
```
$ ./gofasta sam variants -a 7-WU-FF1.gff -s foo.sorted.sam
Error: Error parsing gff SeqID: 7-WU-FF
…
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### Description of the issue:
Using picard `SamFormatConverter` to turn a long-read CRAM to BAM with more than 65536 cigar ops generates a `CG:B:i,` tag. The SAM specification dictates this must …
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```
If you set outSAMattributes as All then the sam file generated is incompatible
with Cufflinks. The error is something like no XS tag for a spliced read. But
when one uses outSAMattributes in st…
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```
What steps will reproduce the problem?
1. bamToBed -i foo.bam -split
on the following foo.bam file
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chr9 LN:124076172
@RG ID:sample1 P…
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## Open API for FSP Interoperability - Change Request
### **Table of Contents**
* [1. Preface](#1.-preface)
* [1.1 Change Request Information](#1.1-change-request-information)
* [2. Problem …