I am implementing a parser that is able to read the BAM file in pairs so whenever I read a record where pos < mpos I search for the mate and I create a pair structure. Once I find the mate I have to roll back to the second read and continue building the pairs. I could create a circular array of BAM records to be filled sequentially and used then to build pairs, but I cannot be 100% sure that the array is large enough to contain the mate record that might be very far in the sorted BAM. Do you see what I mean? cheers, Claudio
On 07/12/2015 19:12, James Bonfield wrote: > On Mon, Dec 07, 2015 at 06:03:45PM +0100, Claudio Alberti wrote: >> it seems that bgzf_seek and bgzf_tell work better even if I get a >> crash after about 43000 reads... > "Better" isn't good though if it still crashes. > > Fundamentally, if you're using bgzf_tell/seek then you have to do all > I/O at the bgzf level and never call something on the higher level > hts_file API. This means losing some other functionality. > > What is it you're trying to achieve here? > > I guess the reason this isn't a problem for most people is that > tell/seek isn't that useful for most applications. Yes it offers a > way of going to specific file locations, but usually tools want > specific genomic locations instead. Eg fetch me all the data for this > gene or split by chromosome. > > These are dealt with using iterators and the bam/cram indices. > They're well tested and used by many samtools components, unlike > tell/seek which are more internal things. > > I can see some benefits to the file level slicing too (eg in some > parallel processing techniques), so I think it's something we need to > get working robustly, but not at top priority right now. > > James > -- Claudio Alberti ---------------------------------------------- EPFL SCI STI MM ELG 140 (ELG Building) Station 11 CH-1015 Lausanne - Switzerland Tel. +41 21 6936869 ---------------------------------------------- ------------------------------------------------------------------------------ Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
