Feature request - add option to sort by query name like Picard #369
Description
Hi,
I think it could be a good thing to make sambamba query-name sort be compatible with other Picard tools. I wrote a quick implementation of this in BioD/bio/bam/reader.d (based on https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java)
bool compareReadNames(R1, R2)(const auto ref R1 a1, const auto ref R2 a2)
if (isBamRead!R1 && isBamRead!R2)
{
if(a1.name == a2.name)
{
if(a1.is_paired() || a2.is_paired())
{
if(!a1.is_paired())
return false;
if(!a2.is_paired())
return true;
if(a1.is_first_of_pair() && a2.is_second_of_pair())
return true;
if(a1.is_second_of_pair() && a2.is_first_of_pair())
return false;
}
if(a1.strand() != a2.strand())
{
return a1.strand() == '-' ? false : true;
}
if(a1.is_secondary_alignment() != a2.is_secondary_alignment())
{
return a2.is_secondary_alignment();
}
if(a1.is_supplementary() != a2.is_supplementary())
{
return a2.is_supplementary();
}
if(!a1["HI"].is_nothing)
{
if(a2["HI"].is_nothing)
return true;
int i1 = to!int(a1["HI"]);
int i2 = to!int(a2["HI"]);
return i1 < i2;
}
else
if(!a2["HI"].is_nothing)
return false;
}
return a1.name < a2.name;
}
But I'm very new to the field of bioinformatics and I'm using the D language for the first time, so that is why I've decided not to use the Pull-request.
I'm open for any kind of collaboration as long as I can get some guidence in D language.
Thank you,
Timur