Re: [Samtools-devel] samtools sort -o

[Joel M. <j_m...@lb...>]

put them in TMPDIR and give a heads up that TMPDIR should be set to a
large scratch partition.  If they've been working in genomics long
they've probably already done that.

Joel

On Wed, Feb 27, 2013 at 7:43 AM, Heng Li <lh...@sa...> wrote:
> Probably a better way is to use mkstemp(), but I am worrying that the temporary file names may look less meaningless. There is also a concern that if we put temporary files in /tmp by default, sorting may fail on machines that do not have a large /tmp partition.
>
> Heng
>
> On Feb 26, 2013, at 4:58 AM, David K Jackson wrote:
>
>> On 21/02/13 11:10, James Bonfield wrote:
>>> Hello all,
>>>
>>> Just a very minor bug report for samtools sort:
>>>
>>> The samtools sort manual states.
>>>
>>>  samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
>>>
>>> Sort alignments by leftmost coordinates. File <out.prefix>.bam will be
>>> created. This command may also create temporary files
>>> <out.prefix>.%d.bam when the whole alignment cannot be fitted into
>>> memory (controlled by option -m).
>>>
>>> OPTIONS:
>>> -o   Output the final alignment to the standard output.
>>> -n   Sort by read names rather than by chromosomal coordinates
>>> -m INT       Approximately the maximum required memory. [500000000]
>>>
>>> The command line parsing though seems broken if you use -o. Use of -o
>>> does indeed force it to output to stdout, but a filename is still
>>> required to be specified (and ignored).
>>>
>>> It should be modified so that out.prefix is not needed when -o is
>>> used.
>>>
>> Hi James - it is not ignored: the prefix is used for temporary files
>> generated even when final output is sent to stdout.
>> David
>>
>>
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>
>
> --
>  The Wellcome Trust 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.
>
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