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cbg-ethz / haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
GNU General Public License v3.0
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How set the number of threads? #40

Closed seoanezonjic closed 6 years ago

seoanezonjic commented 7 years ago

I'm using the last release of hapliclique and I had seen that use pthreads. How can I set more than one thread to do the analysis? Thanks Pedro

brnrdlang commented 7 years ago

The old version of Haploclique did parallelization by simply partitioning the reads in several datasets, and then running haploclique with GNU parallel on every dataset. This meant that edges between reads in different partitions were not considered for the first iteration of clique enumeration, leading to some loss of information. After rewriting the original bash script handling the iterations directly into the C++ code, the parallelization part of the script didn't make it into the new version.

armintoepfer commented 7 years ago

The remark about losing information in the old version is wrong.

Too bad that parallelization didn't make it.

On Apr 3, 2017 11:57 PM, "Bernhard Lang" notifications@github.com wrote:

The old version of Haploclique did parallelization by simply partitioning the reads in several datasets, and then running haploclique with GNU parallel on every dataset. This meant that edges between reads in different partitions were not considered for the first iteration of clique enumeration, leading to some loss of information. After rewriting the original bash script handling the iterations directly into the C++ code, the parallelization part of the script didn't make it into the new version.

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