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Id: 116702
Status: new
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Queue: Bio-SamTools

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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 [...]
From: Kevin Buckley < [...]>
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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 ?

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