Daniel Cameron
Daniel Cameron
The FASTQ parsing is currently tightly coupled with spades output. Simple nodes with no intra-sequence branching fail to load. It appears this is due to shapes-specific parsing of node names...
Hello I am looking at adding GRIDSS to parliament, but it appears that survivor does not support GRIDSS output. AFAIK, GRIDSS is fully compliant with VCFv4.3 but there are a...
bwa silently ignores reads in fastq files in which the length of the read quals does not match the length of the read sequence. Could a special case be added...
I am attempting to read from a BAM file stored in a GCE bucket that is configured as user pay and get the following error: ``` $ samtools view -H...
### Description of the issue: Validation of specifications-compliant unmapped records raises validation failures. The SAM specifications state: • Bit 0x4 is the only reliable place to tell whether the read...
### Description The existing aysnc read code performs read-ahead and decompression on a seperate thread. Combining with AsyncBufferedIterator and we can get ~3x performance increase when doing light processing (eg....
Unnecessary IllegalStateException "no sequences were added to the reference" in FastaReferenceWriter
### Description of the issue: FastaReferenceWriter throws an exception if no sequences were written: ``` Exception in thread "main" java.lang.IllegalStateException: no sequences were added to the reference at htsjdk.samtools.reference.FastaReferenceWriter.close(FastaReferenceWriter.java:635) ```...
## Question I've been poring over the documentation and I'm still can't work out if I can use the FM-index API for string graph construction (in a similar manner to...
Are there any plans to support symbolic SVs, or SVs in breakend notation? To properly compare such variants requires haplotype reconstruction as equivalent representations can be quite different. For example,...
The SAM specifications does not specify the encoding of the header. S1 states `Unless explicitly specified elsewhere, all fields are encoded using 7-bit US-ASCII` S1 states that alignment lines have...