Subject: | Re: Bio-SamTools-1.43 is confused about what various SAMtools build dirs supply where - and so am I |
Date: | Thu, 4 Aug 2016 14:30:49 +1200 |
To: | bug-Bio-SamTools [...] rt.cpan.org |
From: | Kevin Buckley <kevin.buckley.ecs.vuw.ac.nz [...] gmail.com> |
Bit more info gleaned about this
In the
bam.h
file that's in the top build directory for samtools-1.3, I read
---8<---------8<---------8<---------8<---------8<---------8<---------8<---------8<---------8<----
@discussion Notes:
1. qname is zero tailing and core.l_qname includes the tailing '\0'.
2. l_qseq is calculated from the total length of an alignment block
on reading or from CIGAR.
3. cigar data is encoded 4 bytes per CIGAR operation.
4. seq is nybble-encoded according to bam_nt16_table.
*/
// typedef struct { ... } bam1_t;
// NOTE htslib version doesn't have l_aux; use bam_get_l_aux(b) instead
#ifndef SAMTOOLS_HTSLIB_SUPPRESS_HACKS
// NOTE htslib also renames data_len to l_data; this macro may help or hinder
---8<---------8<---------8<---------8<---------8<---------8<---------8<---------8<---------8<----
so the missing member really isn't there by design.
So which version of SAMtools should Bio-SamTools-1.43 be compiled against ?