From d759891e93052f81eb9a0b9cde30ccd1552b6f56 Mon Sep 17 00:00:00 2001 From: waynebhayes Date: Wed, 17 Jul 2019 22:02:48 -0700 Subject: [PATCH] retype README.md --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index b4de35f5..bc323947 100755 --- a/README.md +++ b/README.md @@ -56,7 +56,8 @@ This method is the fastest *per sample*, and in the long run is also guaranteed AR is a horrendously slow but asymptotically correct method of picking *k* nodes uniformly at random, and accepting the sample only if the *k* nodes form a connected graphlet. For large values of *k* and for most typical input networks that are sparse, this results in the vast majority of *k*-node sets being rejected. This method is not recommended since it is exponentially slow with large values of *k*. ### Optional command-line arguments -#### -t*N*: run BLANT in parallel mode with *N* threads. For all modes except indexing (-mi) mode, speedup should be linear (this has been tested on a machine with 64 cores, and speedup is linear.) However, with indexing mode, the processes are I/O bound and speedup is only linear up to about 8 threads, and little speedup is observed beyond 8 threads. +#### -t*N*: run BLANT in parallel mode with *N* threads. +For all modes except indexing (-mi) mode, speedup should be linear (this has been tested on a machine with 64 cores, and speedup is linear.) However, with indexing mode, the processes are I/O bound and speedup is only linear up to about 8 threads, and little speedup is observed beyond 8 threads. #### -d*m*: displayMode Display mode determines how the graphlet ID of the sampled graphlet is displayed: default is *i*, BLANT's internal integer ordinal of the canonical (order similar to that described in [Hasan, Chung, Hayes 2017](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181570) except using the lower rather than upper triangle, to be more compatible with [Jesse](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147078). Other formats include *d*, the decimal value of the canonical; *b* the same integer dispalyed as binary; *j* use Jesse's ID; and *o* use ORCA's ID.