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
