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I am trying to run bwa on a computer based on an intel i7 processor with 8gb of RAM and running Fedora 11.
The program compiles but with warnings:
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gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bntseq.c -o bntseq.o
bntseq.c: In function ‘bns_restore’:
bntseq.c:98: warning: format ‘%lld’ expects type ‘long long int *’, but argument 3 has type ‘int64_t *’
bntseq.c:113...
2009-09-29 09:06:08 UTC by nobody
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Line #97 solid2fastq.pl should be:
die(qq/** unmatched read name: '$_' != '$t''\n/) unless ($_ eq $t);
A bug occurs if the number of comment lines are not equal in the .csfasta and .qual file.
2009-09-05 17:29:23 UTC by nilshomer
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Line 97 in solid2fastq.pl should be:
die(qq/** unmatched read name: '$_' != '$t''\n/) unless ($_ eq $t);
This occurs if the # of comments is not the same in the .csfasta and .qual files.
2009-09-05 17:28:21 UTC by nobody
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I've added this patch to the bug-tracker system, but it may be worth to post it here instead...
Basically adds a new predicate (ill2sanger) to convert illumina fastq to sanger fastq.
2009-08-20 15:35:24 UTC by daweonline
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In mapping, maq has a random behaviour which may affect a tiny fraction of reads in a uniform way. It occrs very rarely. I would suggest ignoring this in general.
2009-08-20 11:32:22 UTC by lh3lh3
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I will add one in future. It should be something as simple as "Type 'make' to compile bwa and copy the binary anywhere you like.".
2009-08-20 11:00:17 UTC by lh3lh3
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I have a mac laptop and routinely compile and run it on my laptop. Could you try to "make clean" and then "make" again? You may also try to run "ranlib bwt_gen/libbwtgen.a" to create the library index. Hope that works.
2009-08-20 10:59:08 UTC by lh3lh3
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I am also thinking to separate the two projects when most of the active developments mainly happen in BWA. Thanks for the suggestion.
2009-08-20 10:57:02 UTC by lh3lh3
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This is a known bug and I believe it has been fixed in the latest release and so I am going to close this ticket. Thanks anyway.
2009-08-20 10:55:12 UTC by lh3lh3
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BWA was first started from my local SVN. When I released it at sourceforge, I did not want to lose all the historical records and therefore I have not put it at SourceForge.
2009-08-20 10:53:39 UTC by lh3lh3
