Ah, thanks for pointing out the tabs issue, I fixed my exporter to match the spec. I found and fixed my issue as well which turns out was unrelated to htslib. :-)
-Will On Fri, Nov 16, 2018 at 4:26 AM James Bonfield <j...@sanger.ac.uk> wrote: > Hello Will, > > Sorry for the slow reply. > > On Fri, Nov 09, 2018 at 09:43:46PM -0500, Will Stokes wrote: > > [W::bam_hdr_read] EOF marker is absent. The input is probably truncated > > This is a confusing message. > > It's claiming EOF marker is absent, but I don't think it is. > I suspect it's due to the @HD line using spaces instead of tabs and > triggering something else. > > For me samtools reads your file just fine, despite the broken header. > > Scramble correctly reports the missing tab and Picard reports a > malformed header. > > > In order to write the SAM/BAM files I make the following calls: > > > > sam_open > > > > sam_hdr_write > > > > sam_write1 > > > > sam_close > > That looks fine to me. > > > This is with the most recent release of htslib. When writing a BAM file I > > find: > > > > > > outputFile->format.compression = 2 > > > > outputFile->format.compression_level = -1 > > Level -1 just means default zlib compression. > > The compression value is the htsCompression enum with 2 being bgzf, > which is correct. > > > From reading the SAM/BAM specification it sounds like I'm missing a 28 > byte > > EOF at the end of my file. Am I expeted to write those 1f 8b .. 00 00 > bytes > > myself manually, or was htslib supposed to have done that for me, or is > > there some htslib command I have failed to call? > > No, the close will do it for you. > > > Note reading the header for this file works, but sam_read1 fails so I > > cannot parse the various reads. > > Odd that I don't see this with "samtools view" nor htslib/test_view. > > James > > -- > James Bonfield (j...@sanger.ac.uk) > The Sanger Institute, Hinxton, Cambs, CB10 1SA > > > -- > The Wellcome Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > > > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help >
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