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Search: Posts Made By: jmarshall
Forum: Bioinformatics 10-21-2016, 06:14 AM
Replies: 3
Views: 4,749
Posted By jmarshall
You're telling samtools it may only use quite a...

You're telling samtools it may only use quite a small memory buffer, so it is using many many temporary files instead. You may wish to reread the documentation and use (say) `-m 2G` instead.
...
Forum: Bioinformatics 10-12-2016, 03:08 AM
Replies: 6
Views: 2,379
Posted By jmarshall
GapFiller's src/Makefile.am has been updated to...

GapFiller's src/Makefile.am has been updated to account for a linking change in the last few years (cf ld --add-needed), but unfortunately the rest of its build infrastructure has not been...
Forum: Bioinformatics 08-31-2016, 12:01 AM
Replies: 5
Views: 2,452
Posted By jmarshall
A new machine crashing like this under this sort...

A new machine crashing like this under this sort of load suggests bad RAM. Go get MemTest86 and run it overnight.
Forum: Bioinformatics 08-05-2016, 02:40 AM
Replies: 4
Views: 5,884
Posted By jmarshall
That error message identifies duplicate sample...

That error message identifies duplicate sample names, or to find them all at once:

bcftools view -h file.bcf|grep '^#CHROM'| cut -f10-|tr '\t' '\n'|sort|uniq -c|grep -v '^ *1 '

Then you could...
Forum: Bioinformatics 08-05-2016, 02:05 AM
Replies: 4
Views: 5,884
Posted By jmarshall
Sample names are parsed from the #CHROM POS ...

Sample names are parsed from the #CHROM POS ID REF line, and can't appear more than once (at least for bcftools's implementation; not sure if this is clear in the VCF spec).

The actual...
Forum: Bioinformatics 06-22-2016, 10:02 AM
Replies: 13
Views: 7,189
Posted By jmarshall
I expect that it will indeed be bundled within...

I expect that it will indeed be bundled within the next bcftools release.
Forum: Bioinformatics 06-22-2016, 08:19 AM
Replies: 13
Views: 7,189
Posted By jmarshall
That only partially compiled it (to be precise,...

That only partially compiled it (to be precise, it did not link it).

To compile this plugin properly, you need to reproduce the commands that are used to compile the other plugins. So you should...
Forum: Bioinformatics 03-16-2016, 05:28 AM
Replies: 4
Views: 2,228
Posted By jmarshall
Re #2, compiling bedtools 2.25.0 with Intel's...

Re #2, compiling bedtools 2.25.0 with Intel's icpc (ICC) 15.0.0 20140723 I got only a handful of trivial warnings (see https://github.com/arq5x/bedtools2/pull/382). If your warnings are similar, I...
Forum: Bioinformatics 02-08-2016, 02:29 AM
Replies: 6
Views: 5,131
Posted By jmarshall
The information Richard quoted from samtools 1.1...

The information Richard quoted from samtools 1.1 has been superseded in samtools 1.3.

First off, system packages like the ncurses development package libncurses5-dev are non-science-related...
Forum: Bioinformatics 08-18-2015, 12:13 AM
Replies: 3
Views: 2,019
Posted By jmarshall
Windows refuses to create files or directories...

Windows refuses to create files or directories with names like aux, as it reserves such filenames to refer to IIRC your serial port.

So alas you're straight out of luck with 2.24.0 on Windows. ...
Forum: Bioinformatics 08-17-2015, 11:50 PM
Replies: 16
Views: 6,626
Posted By jmarshall
On RPM-based distributions, this package is often...

On RPM-based distributions, this package is often called ncurses-devel.
Forum: Bioinformatics 08-07-2015, 04:19 AM
Replies: 4
Views: 2,268
Posted By jmarshall
The additional -s wrinkle has been fixed...

The additional -s wrinkle has been fixed (https://github.com/samtools/samtools/commit/8054f3716dc0949e00fb7bcb899c2a0726cea2ef) since samtools 1.0.

Thanks for the reminder to revisit the main...
Forum: Bioinformatics 06-18-2015, 01:04 AM
Replies: 2
Views: 1,759
Posted By jmarshall
Current bcftools 1.x contains two calling...

Current bcftools 1.x contains two calling methods: call -c is the original bcftools consensus caller, while call -m is a more recent multi-allelic caller. Only the consensus caller outputs FQ.

If...
Forum: Bioinformatics 06-16-2015, 01:43 AM
Replies: 19
Views: 22,751
Posted By jmarshall
The problem with scaffold_28 in this file was the...

The problem with scaffold_28 in this file was the same problem that was reported here (http://seqanswers.com/forums/showpost.php?p=172494&postcount=6). It has now been fixed, and the fix will appear...
Forum: Bioinformatics 06-02-2015, 10:58 PM
Replies: 6
Views: 7,723
Posted By jmarshall
Thanks for reporting this. I've now fixed it...

Thanks for reporting this. I've now fixed it (https://github.com/samtools/htslib/commit/1980e5859251741f7905e754c07112a0fe3ec3e5) and the fix will appear in samtools (and htslib) 1.3.
Forum: Bioinformatics 04-22-2015, 02:20 AM
Replies: 2
Views: 1,488
Posted By jmarshall
I build it every day on 64-bit Linux without any...

I build it every day on 64-bit Linux without any issues.

Perhaps you could show us a sampling of these inconsistent .h file location and type redefinition error messages.
Forum: Bioinformatics 03-16-2015, 01:45 AM
Replies: 4
Views: 2,748
Posted By jmarshall
If the error you get when building bedtools (or...

If the error you get when building bedtools (or other software) is



then on Cygwin the package you need to ensure is installed is zlib-devel.
Forum: Bioinformatics 03-05-2015, 02:51 AM
Replies: 6
Views: 2,338
Posted By jmarshall
There's a bug in bwa here: in main() in main.c it...

There's a bug in bwa here: in main() in main.c it ought to sanitise argv[i] (say, by changing tabs and newlines to spaces) before adding it to the @PG header. (And similarly argv[0] really.)

As...
Forum: Bioinformatics 11-24-2010, 08:01 AM
Replies: 13
Views: 14,183
Posted By jmarshall
You don't say what operating system,...

You don't say what operating system, distribution, or release thereof you're running on, or whether you built cufflinks yourself or downloaded a binary.

However, you would see this message if, for...
Forum: Bioinformatics 11-17-2010, 07:41 AM
Replies: 6
Views: 5,663
Posted By jmarshall
checking if gcc accepts -m64... yes [...] --...

checking if gcc accepts -m64... yes
[...]
-- tophat 1.1.0 Configuration Results --
C compiler: gcc -Wall -m64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/usr/local/include
[...]...
Forum: Bioinformatics 10-28-2010, 12:21 AM
Replies: 27
Views: 32,279
Posted By jmarshall
The -Dexpl[etc] flags need to be in action when...

The -Dexpl[etc] flags need to be in action when bam_maqcns.c is compiled. (And in the just-released samtools 0.1.9, also when errmod.c is compiled.) You probably have a faulty bam_maqcns.o lying...
Forum: Bioinformatics 10-27-2010, 12:52 PM
Replies: 84
Views: 31,670
Posted By jmarshall
You are using Intel's compiler and you have...

You are using Intel's compiler and you have configured cufflinks so as to compile with -Werror.

This is a relatively useless warning, and it's hard to see why it's being triggered by this code. ...
Forum: Bioinformatics 10-27-2010, 11:26 AM
Replies: 27
Views: 32,279
Posted By jmarshall
The Cygwin folks changed the way they install...

The Cygwin folks changed the way they install ncurses a while back; see http://www.cygwin.com/ml/cygwin-announce/2010-01/msg00002.html.

Hence you should add -I/usr/include/ncurses to CFLAGS in the...
Forum: Bioinformatics 10-26-2010, 12:50 AM
Replies: 4
Views: 5,334
Posted By jmarshall
Tabix parses its command line options with...

Tabix parses its command line options with getopt(). On Linux, you get GNU getopt() which, as a convenient extension to the standard behaviour, accepts options intermixed with arguments such as...
Forum: Bioinformatics 09-17-2010, 01:13 AM
Replies: 4
Views: 11,290
Posted By jmarshall
The hint from samtools view is telling you that...

The hint from samtools view is telling you that '--' is being interpreted as a tag, which means that it is immediately following a tab character each time it appears.

SAM header fields are...
Showing results 1 to 25 of 39

 

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