nicholasferguson/ld-spatt

LD-SPATT (spatt, statistics for patterns) gsl 2.1 on Win64. VC2015. ported to win64. Large Deviation on coin tosses in s/h. And on Markov Sequences in C++ code.. Also excel s/h

#Introduction

• Spatt includes some 'Large Deviation' samples. Migrated this over to win64 to play with those samples
• Included latest gsl at this time.
• Added a large deviation example, on coin tosses, as an excel spreadsheet.

#Library folder's structure

• \gsl-2.1-src -
• \gsl-2.1-src\VC14 - (open libgsl.sln)
• \spatt-1.2.2.t3 - (open spatt-1.2.2.t3.sln)

#Build Instructions

• Build libgsl.sln first. Review that configuration is for a x64 build. This creates a new directory with required include files \gsl-2.1-src\gsl ( this subdirectory is created during this build)
• for gsl-2.1-src, I did not run full regression tests
• Only test was whether it worked with spatt-1.2.2.t3
• Build spatt-1.2.2.t3.sln
• Used VC14 (Visual Studio 2015)
• VC14, Update 1 works fine with relative paths.Previous release was buggy.

#Changes to original code. Spatt

• In spatt-1.2.2.t3\src are several file names, renamed with prefix 'main'. Each of these have a int main function. These are test files. In VC14, Solution Explorer, you can include or exclude as to test.

#Changes to original code. gsl

See file "Changes.to.gsl-2.1.to.build.in.VC14.64.bat.txt"

#Output from: hiv.fasta -l 4 -m 1 -V --all-words --max-pvalue 0.1 > test_result_ldspatt.txt

count length 4 Markov order 1 specified length("hiv.fasta") 10901 includes white spaces count memory usage (bytes) 1360 sequence length 9718 w/o white spaces

pattern nobs natt stat aaac 42 59.66 -1.314358 aaat 96 75.83 1.14361 aacc 26 42.62 -1.677783 aagg 64 93.14 -2.368286 aatt 83 58.88 1.998653 agaa 148 115.55 1.851555 aggc 33 55.08 -2.319139 aggt 25 52.06 -3.910779 agta 96 59 4.271916 agtc 17 29.5 -1.382496 agtt 33 47.27 -1.081144 atcc 38 26.25 1.022044 atga 50 67.27 -1.066825 atgc 22 37.49 -1.669311 caaa 65 84.52 -1.129944 ccaa 40 60.38 -1.766736 cccg 14 5.15 2.246298 cgta 1 5.47 -1.207353 ctaa 30 48.44 -1.821535 ctgt 45 23.35 3.495926 ctta 24 37.61 -1.25949 gaca 78 60.48 1.055798 gagg 47 68.66 -1.655312 gagt 31 44.88 -1.075787 gcac 22 33.71 -1.034677 ggaa 103 74.56 2.226494 ggcg 14 6.83 1.249208 gtac 42 22.46 3.006728 gtag 59 41 1.499082 gtcc 5 15.9 -2.245011 gtga 23 40.74 -2.041267 gtgg 50 32.84 1.665666 gttc 9 17.29 -1.060902 gttg 18 29.82 -1.18263 taag 36 66.93 -3.903585 tagg 42 57.25 -1.012561 tagt 64 37.41 3.340595 tcat 19 32.04 -1.343134 tctg 40 24.7 1.769076 tctt 12 22.94 -1.368687 tgaa 33 66.52 -4.699309 tgag 35 61.26 -3.0141 tgga 84 56.89 2.564963 tggg 62 45.86 1.154112 tgtg 48 29.3 1.987367 ttga 28 51.66 -2.919791