v1.8.6 commit. bug fix, distance prioritization, graph features, dire…

…ctory cleanup When pipelined with the ARCS/ARKS scaffolder, LINKS v1.8.6 prioritizes paths with shorter gaps only when there are no ambiguous gaps distances with the neighboring sequences considered. Add linkage information (ID and size) to the output .gv graph. We now provide a utility (./tools/consolidateGraphs.pl) to highlight differences between two LINKS graphs. Implement -z min_size with an ARCS checkpoint.
bcgsc · Mar 13, 2018 · 9a5424b · 9a5424b
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 # LINKS
 
 ## Long Interval Nucleotide K-mer Scaffolder
-## LINKS v1.8.5 Rene L. Warren, 2014-2017
+## LINKS v1.8.6 Rene L. Warren, 2014-2018
 ## email: rwarren [at] bcgsc [dot] ca
 ## Visit www.bcgsc.ca/bioinfo/software/links for additional information
 
@@ -15,6 +15,13 @@ LINKS is a genomics application for scaffolding genome assemblies with long
 reads, such as those produced by Oxford Nanopore Technologies Ltd.
 It can be used to scaffold high-quality draft genome assemblies with any long
 sequences (eg. ONT reads, PacBio reads, another draft genomes, etc)
+It is used to scaffold contig pairs linked by ARCS/ARKS.
+
+
+### What's new in v1.8.6 ?
+---------------------
+
+When pipelined with the ARCS/ARKS scaffolder, LINKS v1.8.6 prioritizes paths with shorter gaps only when there are no ambiguous gaps distances with the neighboring sequences considered. Add linkage information (ID and size) to the output .gv graph. We now provide a utility (./tools/consolidateGraphs.pl) to highlight differences between two LINKS graphs. Implement -z min_size with an ARCS checkpoint.
 
 
 ### What's new in v1.8.5 ?

diff --git a/bin/LINKS b/bin/LINKS
diff --git a/links_v1-5-1.tar.gz → releases/binaries/links_v1-5-1.tar.gz b/links_v1-5-1.tar.gz → releases/binaries/links_v1-5-1.tar.gz
diff --git a/links_v1-5-2.tar.gz → releases/binaries/links_v1-5-2.tar.gz b/links_v1-5-2.tar.gz → releases/binaries/links_v1-5-2.tar.gz
diff --git a/links_v1-5.tar.gz → releases/binaries/links_v1-5.tar.gz b/links_v1-5.tar.gz → releases/binaries/links_v1-5.tar.gz
diff --git a/links_v1-6-1.tar.gz → releases/binaries/links_v1-6-1.tar.gz b/links_v1-6-1.tar.gz → releases/binaries/links_v1-6-1.tar.gz
diff --git a/links_v1-6.tar.gz → releases/binaries/links_v1-6.tar.gz b/links_v1-6.tar.gz → releases/binaries/links_v1-6.tar.gz
diff --git a/links_v1-7.tar.gz → releases/binaries/links_v1-7.tar.gz b/links_v1-7.tar.gz → releases/binaries/links_v1-7.tar.gz
diff --git a/links_v1-8-1.tar.gz → releases/binaries/links_v1-8-1.tar.gz b/links_v1-8-1.tar.gz → releases/binaries/links_v1-8-1.tar.gz
diff --git a/links_v1-8-2.tar.gz → releases/binaries/links_v1-8-2.tar.gz b/links_v1-8-2.tar.gz → releases/binaries/links_v1-8-2.tar.gz
diff --git a/links_v1-8-3.tar.gz → releases/binaries/links_v1-8-3.tar.gz b/links_v1-8-3.tar.gz → releases/binaries/links_v1-8-3.tar.gz
diff --git a/links_v1-8-4.tar.gz → releases/binaries/links_v1-8-4.tar.gz b/links_v1-8-4.tar.gz → releases/binaries/links_v1-8-4.tar.gz
diff --git a/links_v1-8-5.tar.gz → releases/binaries/links_v1-8-5.tar.gz b/links_v1-8-5.tar.gz → releases/binaries/links_v1-8-5.tar.gz
diff --git a/releases/binaries/links_v1-8-6.tar.gz b/releases/binaries/links_v1-8-6.tar.gz
diff --git a/links_v1-8.tar.gz → releases/binaries/links_v1-8.tar.gz b/links_v1-8.tar.gz → releases/binaries/links_v1-8.tar.gz
diff --git a/links_v1.8.4/LINKS → releases/links_v1.8.4/LINKS b/links_v1.8.4/LINKS → releases/links_v1.8.4/LINKS
diff --git a/links_v1.8.4/LINKS-readme.pdf → releases/links_v1.8.4/LINKS-readme.pdf b/links_v1.8.4/LINKS-readme.pdf → releases/links_v1.8.4/LINKS-readme.pdf
diff --git a/links_v1.8.4/LINKS-readme.txt → releases/links_v1.8.4/LINKS-readme.txt b/links_v1.8.4/LINKS-readme.txt → releases/links_v1.8.4/LINKS-readme.txt
diff --git a/links_v1.8.4/LINKS.pl → releases/links_v1.8.4/LINKS.pl b/links_v1.8.4/LINKS.pl → releases/links_v1.8.4/LINKS.pl
diff --git a/...8.4/test/LINKSrecipe_athaliana_ectools.sh → ...8.4/test/LINKSrecipe_athaliana_ectools.sh b/...8.4/test/LINKSrecipe_athaliana_ectools.sh → ...8.4/test/LINKSrecipe_athaliana_ectools.sh
diff --git a/..._v1.8.4/test/LINKSrecipe_athaliana_raw.sh → ..._v1.8.4/test/LINKSrecipe_athaliana_raw.sh b/..._v1.8.4/test/LINKSrecipe_athaliana_raw.sh → ..._v1.8.4/test/LINKSrecipe_athaliana_raw.sh
diff --git a/...4/test/LINKSrecipe_pglaucaPG29-WS77111.sh → ...4/test/LINKSrecipe_pglaucaPG29-WS77111.sh b/...4/test/LINKSrecipe_pglaucaPG29-WS77111.sh → ...4/test/LINKSrecipe_pglaucaPG29-WS77111.sh
diff --git a/links_v1.8.4/test/runIterativeLINKS_ECK12.sh → ...ks_v1.8.4/test/runIterativeLINKS_ECK12.sh b/links_v1.8.4/test/runIterativeLINKS_ECK12.sh → ...ks_v1.8.4/test/runIterativeLINKS_ECK12.sh
diff --git a/...v1.8.4/test/runIterativeLINKS_ECK12A2D.sh → ...v1.8.4/test/runIterativeLINKS_ECK12A2D.sh b/...v1.8.4/test/runIterativeLINKS_ECK12A2D.sh → ...v1.8.4/test/runIterativeLINKS_ECK12A2D.sh
diff --git a/...v1.8.4/test/runIterativeLINKS_ECK12raw.sh → ...v1.8.4/test/runIterativeLINKS_ECK12raw.sh b/...v1.8.4/test/runIterativeLINKS_ECK12raw.sh → ...v1.8.4/test/runIterativeLINKS_ECK12raw.sh
diff --git a/..._v1.8.4/test/runIterativeLINKS_SCS288c.sh → ..._v1.8.4/test/runIterativeLINKS_SCS288c.sh b/..._v1.8.4/test/runIterativeLINKS_SCS288c.sh → ..._v1.8.4/test/runIterativeLINKS_SCS288c.sh
diff --git a/...s_v1.8.4/test/runIterativeLINKS_SCW303.sh → ...s_v1.8.4/test/runIterativeLINKS_SCW303.sh b/...s_v1.8.4/test/runIterativeLINKS_SCW303.sh → ...s_v1.8.4/test/runIterativeLINKS_SCW303.sh
diff --git a/links_v1.8.4/test/runIterativeLINKS_STH58.sh → ...ks_v1.8.4/test/runIterativeLINKS_STH58.sh b/links_v1.8.4/test/runIterativeLINKS_STH58.sh → ...ks_v1.8.4/test/runIterativeLINKS_STH58.sh
diff --git a/links_v1.8.4/test/runall.sh → releases/links_v1.8.4/test/runall.sh b/links_v1.8.4/test/runall.sh → releases/links_v1.8.4/test/runall.sh
diff --git a/links_v1.8.4/test/runme_EcoliK12iterative.sh → ...ks_v1.8.4/test/runme_EcoliK12iterative.sh b/links_v1.8.4/test/runme_EcoliK12iterative.sh → ...ks_v1.8.4/test/runme_EcoliK12iterative.sh
diff --git a/...v1.8.4/test/runme_EcoliK12iterativeA2D.sh → ...v1.8.4/test/runme_EcoliK12iterativeA2D.sh b/...v1.8.4/test/runme_EcoliK12iterativeA2D.sh → ...v1.8.4/test/runme_EcoliK12iterativeA2D.sh
diff --git a/...v1.8.4/test/runme_EcoliK12iterativeRAW.sh → ...v1.8.4/test/runme_EcoliK12iterativeRAW.sh b/...v1.8.4/test/runme_EcoliK12iterativeRAW.sh → ...v1.8.4/test/runme_EcoliK12iterativeRAW.sh
diff --git a/links_v1.8.4/test/runme_EcoliK12single.sh → ...links_v1.8.4/test/runme_EcoliK12single.sh b/links_v1.8.4/test/runme_EcoliK12single.sh → ...links_v1.8.4/test/runme_EcoliK12single.sh
diff --git a/...s_v1.8.4/test/runme_EcoliK12singleMPET.sh → ...s_v1.8.4/test/runme_EcoliK12singleMPET.sh b/...s_v1.8.4/test/runme_EcoliK12singleMPET.sh → ...s_v1.8.4/test/runme_EcoliK12singleMPET.sh
diff --git a/...4/test/runme_ScerevisiaeS288citerative.sh → ...4/test/runme_ScerevisiaeS288citerative.sh b/...4/test/runme_ScerevisiaeS288citerative.sh → ...4/test/runme_ScerevisiaeS288citerative.sh
diff --git a/....4/test/runme_ScerevisiaeW303iterative.sh → ....4/test/runme_ScerevisiaeW303iterative.sh b/....4/test/runme_ScerevisiaeW303iterative.sh → ....4/test/runme_ScerevisiaeW303iterative.sh
diff --git a/...s_v1.8.4/test/runme_StyphiH58iterative.sh → ...s_v1.8.4/test/runme_StyphiH58iterative.sh b/...s_v1.8.4/test/runme_StyphiH58iterative.sh → ...s_v1.8.4/test/runme_StyphiH58iterative.sh
diff --git a/...v1.8.4/tools/makeMPETOutput2EQUALfiles.pl → ...v1.8.4/tools/makeMPETOutput2EQUALfiles.pl b/...v1.8.4/tools/makeMPETOutput2EQUALfiles.pl → ...v1.8.4/tools/makeMPETOutput2EQUALfiles.pl
diff --git a/links_v1.8.4/tools/testBloom.pl → releases/links_v1.8.4/tools/testBloom.pl b/links_v1.8.4/tools/testBloom.pl → releases/links_v1.8.4/tools/testBloom.pl
diff --git a/links_v1.8.4/tools/writeBloom.pl → releases/links_v1.8.4/tools/writeBloom.pl b/links_v1.8.4/tools/writeBloom.pl → releases/links_v1.8.4/tools/writeBloom.pl
diff --git a/links_v1.8.5/LINKS → releases/links_v1.8.5/LINKS b/links_v1.8.5/LINKS → releases/links_v1.8.5/LINKS
diff --git a/links_v1.8.5/LINKS-readme.pdf → releases/links_v1.8.5/LINKS-readme.pdf b/links_v1.8.5/LINKS-readme.pdf → releases/links_v1.8.5/LINKS-readme.pdf
diff --git a/links_v1.8.5/LINKS-readme.txt → releases/links_v1.8.5/LINKS-readme.txt b/links_v1.8.5/LINKS-readme.txt → releases/links_v1.8.5/LINKS-readme.txt
diff --git a/links_v1.8.5/LINKS.pl → releases/links_v1.8.5/LINKS.pl b/links_v1.8.5/LINKS.pl → releases/links_v1.8.5/LINKS.pl
diff --git a/links_v1.8.5/lib.tar.gz → releases/links_v1.8.5/lib.tar.gz b/links_v1.8.5/lib.tar.gz → releases/links_v1.8.5/lib.tar.gz
diff --git a/...8.5/test/LINKSrecipe_athaliana_ectools.sh → ...8.5/test/LINKSrecipe_athaliana_ectools.sh b/...8.5/test/LINKSrecipe_athaliana_ectools.sh → ...8.5/test/LINKSrecipe_athaliana_ectools.sh
diff --git a/..._v1.8.5/test/LINKSrecipe_athaliana_raw.sh → ..._v1.8.5/test/LINKSrecipe_athaliana_raw.sh b/..._v1.8.5/test/LINKSrecipe_athaliana_raw.sh → ..._v1.8.5/test/LINKSrecipe_athaliana_raw.sh
diff --git a/...5/test/LINKSrecipe_pglaucaPG29-WS77111.sh → ...5/test/LINKSrecipe_pglaucaPG29-WS77111.sh b/...5/test/LINKSrecipe_pglaucaPG29-WS77111.sh → ...5/test/LINKSrecipe_pglaucaPG29-WS77111.sh
diff --git a/links_v1.8.5/test/runIterativeLINKS_ECK12.sh → ...ks_v1.8.5/test/runIterativeLINKS_ECK12.sh b/links_v1.8.5/test/runIterativeLINKS_ECK12.sh → ...ks_v1.8.5/test/runIterativeLINKS_ECK12.sh
diff --git a/...v1.8.5/test/runIterativeLINKS_ECK12A2D.sh → ...v1.8.5/test/runIterativeLINKS_ECK12A2D.sh b/...v1.8.5/test/runIterativeLINKS_ECK12A2D.sh → ...v1.8.5/test/runIterativeLINKS_ECK12A2D.sh
diff --git a/...v1.8.5/test/runIterativeLINKS_ECK12raw.sh → ...v1.8.5/test/runIterativeLINKS_ECK12raw.sh b/...v1.8.5/test/runIterativeLINKS_ECK12raw.sh → ...v1.8.5/test/runIterativeLINKS_ECK12raw.sh
diff --git a/..._v1.8.5/test/runIterativeLINKS_SCS288c.sh → ..._v1.8.5/test/runIterativeLINKS_SCS288c.sh b/..._v1.8.5/test/runIterativeLINKS_SCS288c.sh → ..._v1.8.5/test/runIterativeLINKS_SCS288c.sh
diff --git a/...s_v1.8.5/test/runIterativeLINKS_SCW303.sh → ...s_v1.8.5/test/runIterativeLINKS_SCW303.sh b/...s_v1.8.5/test/runIterativeLINKS_SCW303.sh → ...s_v1.8.5/test/runIterativeLINKS_SCW303.sh
diff --git a/links_v1.8.5/test/runIterativeLINKS_STH58.sh → ...ks_v1.8.5/test/runIterativeLINKS_STH58.sh b/links_v1.8.5/test/runIterativeLINKS_STH58.sh → ...ks_v1.8.5/test/runIterativeLINKS_STH58.sh
diff --git a/links_v1.8.5/test/runall.sh → releases/links_v1.8.5/test/runall.sh b/links_v1.8.5/test/runall.sh → releases/links_v1.8.5/test/runall.sh
diff --git a/links_v1.8.5/test/runme_EcoliK12iterative.sh → ...ks_v1.8.5/test/runme_EcoliK12iterative.sh b/links_v1.8.5/test/runme_EcoliK12iterative.sh → ...ks_v1.8.5/test/runme_EcoliK12iterative.sh
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diff --git a/...v1.8.5/test/runme_EcoliK12iterativeRAW.sh → ...v1.8.5/test/runme_EcoliK12iterativeRAW.sh b/...v1.8.5/test/runme_EcoliK12iterativeRAW.sh → ...v1.8.5/test/runme_EcoliK12iterativeRAW.sh
diff --git a/links_v1.8.5/test/runme_EcoliK12single.sh → ...links_v1.8.5/test/runme_EcoliK12single.sh b/links_v1.8.5/test/runme_EcoliK12single.sh → ...links_v1.8.5/test/runme_EcoliK12single.sh
diff --git a/...s_v1.8.5/test/runme_EcoliK12singleMPET.sh → ...s_v1.8.5/test/runme_EcoliK12singleMPET.sh b/...s_v1.8.5/test/runme_EcoliK12singleMPET.sh → ...s_v1.8.5/test/runme_EcoliK12singleMPET.sh
diff --git a/...5/test/runme_ScerevisiaeS288citerative.sh → ...5/test/runme_ScerevisiaeS288citerative.sh b/...5/test/runme_ScerevisiaeS288citerative.sh → ...5/test/runme_ScerevisiaeS288citerative.sh
diff --git a/....5/test/runme_ScerevisiaeW303iterative.sh → ....5/test/runme_ScerevisiaeW303iterative.sh b/....5/test/runme_ScerevisiaeW303iterative.sh → ....5/test/runme_ScerevisiaeW303iterative.sh
diff --git a/...s_v1.8.5/test/runme_StyphiH58iterative.sh → ...s_v1.8.5/test/runme_StyphiH58iterative.sh b/...s_v1.8.5/test/runme_StyphiH58iterative.sh → ...s_v1.8.5/test/runme_StyphiH58iterative.sh
diff --git a/...v1.8.5/tools/makeMPETOutput2EQUALfiles.pl → ...v1.8.5/tools/makeMPETOutput2EQUALfiles.pl b/...v1.8.5/tools/makeMPETOutput2EQUALfiles.pl → ...v1.8.5/tools/makeMPETOutput2EQUALfiles.pl
diff --git a/links_v1.8.5/tools/testBloom.pl → releases/links_v1.8.5/tools/testBloom.pl b/links_v1.8.5/tools/testBloom.pl → releases/links_v1.8.5/tools/testBloom.pl
diff --git a/links_v1.8.5/tools/writeBloom.pl → releases/links_v1.8.5/tools/writeBloom.pl b/links_v1.8.5/tools/writeBloom.pl → releases/links_v1.8.5/tools/writeBloom.pl
diff --git a/releases/links_v1.8.6/LINKS b/releases/links_v1.8.6/LINKS
diff --git a/releases/links_v1.8.6/LINKS.pl b/releases/links_v1.8.6/LINKS.pl