From 4788c3136cb9f3c8f08e5de2ea01f7a335238bad Mon Sep 17 00:00:00 2001 From: alameldin Date: Wed, 25 Feb 2015 16:28:13 -0500 Subject: [PATCH 1/2] renaming the snadbox/ scripts to be lowercase --- ChangeLog | 11 +++++++++++ ...nt_intersection.py => bloom-count-intersection.py} | 0 sandbox/{bloom_count.py => bloom-count.py} | 0 sandbox/{read_aligner.py => read-aligner.py} | 0 4 files changed, 11 insertions(+) rename sandbox/{bloom_count_intersection.py => bloom-count-intersection.py} (100%) rename sandbox/{bloom_count.py => bloom-count.py} (100%) rename sandbox/{read_aligner.py => read-aligner.py} (100%) diff --git a/ChangeLog b/ChangeLog index 1b7c52600f..020d09621e 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,14 @@ +2015-02-25 Hussien Alameldin + + * sandbox/bloom_count.py: renamed to bloom-count.py + * sandbox/bloom_count.pyc: renamed to bloom-count.pyc + * sandbox/bloom_count_intersection.py: renamed to + bloom-count-intersection.py + * sandbox/bloom_count_intersection.pyc: renamed to + bloom-count-intersection.pyc + * sandbox/read_aligner.py: renamed to read-aligner.py + * sandbox/read_aligner.pyc: renamed to read-aligner.pyc + 2015-02-25 Tamer A. Mansour * scripts/normalize-by-median.py: change to the default behavior to diff --git a/sandbox/bloom_count_intersection.py b/sandbox/bloom-count-intersection.py similarity index 100% rename from sandbox/bloom_count_intersection.py rename to sandbox/bloom-count-intersection.py diff --git a/sandbox/bloom_count.py b/sandbox/bloom-count.py similarity index 100% rename from sandbox/bloom_count.py rename to sandbox/bloom-count.py diff --git a/sandbox/read_aligner.py b/sandbox/read-aligner.py similarity index 100% rename from sandbox/read_aligner.py rename to sandbox/read-aligner.py From 3c21d99bdb6fc64063a07a9db5e6e13ecf6a7445 Mon Sep 17 00:00:00 2001 From: alameldin Date: Wed, 25 Feb 2015 17:25:20 -0500 Subject: [PATCH 2/2] updating the README.rst and ChangeLog --- ChangeLog | 4 ---- sandbox/README.rst | 6 +++--- 2 files changed, 3 insertions(+), 7 deletions(-) diff --git a/ChangeLog b/ChangeLog index 020d09621e..89fc64a22f 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,13 +1,9 @@ 2015-02-25 Hussien Alameldin * sandbox/bloom_count.py: renamed to bloom-count.py - * sandbox/bloom_count.pyc: renamed to bloom-count.pyc * sandbox/bloom_count_intersection.py: renamed to bloom-count-intersection.py - * sandbox/bloom_count_intersection.pyc: renamed to - bloom-count-intersection.pyc * sandbox/read_aligner.py: renamed to read-aligner.py - * sandbox/read_aligner.pyc: renamed to read-aligner.pyc 2015-02-25 Tamer A. Mansour diff --git a/sandbox/README.rst b/sandbox/README.rst index aa393a6a31..1dfcc57d75 100644 --- a/sandbox/README.rst +++ b/sandbox/README.rst @@ -63,8 +63,8 @@ Good ideas to rewrite using newer tools/approaches: * assembly-diff.py - find sequences that differ between two assemblies * assembly-diff-2.py - find subsequences that differ between two assemblies -* bloom_count.py - count # of unique k-mers; should be reimplemented with HyperLogLog -* bloom_count_intersection.py - look at unique and disjoint #s of k-mers +* bloom-count.py - count # of unique k-mers; should be reimplemented with HyperLogLog, Renamed from bloom_count.py in commit 4788c31 +* bloom-count-intersection.py - look at unique and disjoint #s of k-mers, Renamed from bloom_count_intersection.py in commit 4788c31. * split-sequences-by-length.py - break up short reads by length To examine: @@ -76,7 +76,7 @@ To examine: * error-correct-pass2.py - new error correction foo * find-unpart.py - something to do with finding unpartitioned sequences * normalize-by-align.py - new error correction foo -* read_aligner.py - new error correction foo +* read-aligner.py - new error correction foo, Renamed from read_aligner.py in commit 4788c31. * uniqify-sequences.py - print out paths that are unique in the graph * write-interleave.py - is this used by any protocol etc?