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Currently, the class needs to maintain a redundant list of identifiers to be thread-safe. This should be fixed. Maybe, this is settled already in the SeqAn base class.
fungs updated
9 years ago
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Is there any instructions around for building bowtie-1.2 with the Intel C++ compiler. I am moving forward slowly by modifying header files, which does not seem to be the optimal solution. Any help in …
ghost updated
6 years ago
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Let's make a man page for vg, and one for each subcommand!
To do this, we need a template man page. I will populate that with a stock transformation of the command's help text. I'm going to assign …
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The issue only seems to occure when length(reference) == length(pattern)
```c++
#include
#include
#include
#include
#include
#include
#include
using namespace seqan;
using nam…
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I am seeing a segmentation fault:
```
$wham_dir/bin/WHAM-BAM -m 2 -q 15 -p 10 -x 4 -t $tbam -f $reflib \
1> ${oprefix}_wham.vcf 2> ${oprefix}_wham.out
Aborted (core dumped)
less ${vcf}.out
INFO: …
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**$ cat bug.cpp**
#include
int main() {
using namespace seqan;
auto s = std::string(100, '\xff');
String myString = s;
using TMyIndex = Index;
…
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Some parameters related to SV have wrong help messages (in `mason_variator --help`). See, e.g., https://github.com/seqan/seqan/blob/ea8071221e7e94be68010fb56b21482a647fe570/apps/mason2/mason_variator.…
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Hello,
when using Pizzly 0.37.3 (SeqAn 2.2.0) and Kallisto 0.43.1 with Ensembl 81 and one gets this error message from Pizzly:
```
Error, could not find any transcript sequences check that the i…
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On Linux, SeqAn seems to need libpthread for multithreaded BAM file I/O (at least). But since commit b09e87e0 (I think; I haven't tried git bisect to verify), using any SeqAn code that needs libpthre…
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To avoid error messages like this when SA construction runs out of space:
```
Asynchronous I/O operation failed (waitFor): "Success"
fildes: 9
buffer: 7f7e3a5d6000
offset: 3298d0000
nbytes: 28000…