BOL

While installing Perl GD module, I got following error 

libgd not found !

I am unable to index fasta file with samtools ! It return "different line length in sequence" error message . How to fix it? 

nc@radha[Downloads] samtools faidx dedup.genome.scf.fasta_assembly.fna []
[fai_build_core] different line length in sequence 'jcf7180000001219'.
Could not build fai index dedup.genome.scf.fasta_assembly.fna.fai
nc@radha[Downloads] more dedup.genome.scf.fasta_assembly.fna| grep ">" | wc -l
336

How to Plot a circular overlapping plots, as shown in pic. ?

https://cloud.githubusercontent.com/assets/90373/13977453/0ba63268-f0ef-11e5-9b1b-6b0aa587e3ac.jpg

I tried following table to plot on http://mkweb.bcgsc.ca/tableviewer/

data C D
A 7 18
B 5 15

and it return http://mkweb.bcgsc.ca/tableviewer/tmp/fvufmlm/results/circos-table-fvufmlm-large.png but it does not support overlaps. Any suggestions ?

> install.packages(c('ddalpha', 'recipes')) 

  There is a binary version available but the source version is later:

        binary  source needs_compilation

ddalpha  1.3.1 1.3.1.1              TRUE

Do you want to install from sources the package which needs compilation?

y/n: y

trying URL 'https://mirrors.nic.cz/R/bin/macosx/el-capitan/contrib/3.4/recipes_0.1.2.tgz'

Content type 'application/octet-stream' length 998818 bytes (975 KB)

==================================================

downloaded 975 KB

The downloaded binary packages are in

/tmp/RtmpUg5Cs2/downloaded_packages

installing the source package ‘ddalpha’

trying URL 'https://mirrors.nic.cz/R/src/contrib/ddalpha_1.3.1.1.tar.gz'

Content type 'application/octet-stream' length 543279 bytes (530 KB)

==================================================

downloaded 530 KB

* installing *source* package ‘ddalpha’ ...

** package ‘ddalpha’ successfully unpacked and MD5 sums checked

** libs

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c AlphaProcedure.cpp -o AlphaProcedure.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Common.cpp -o Common.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c DKnn.cpp -o DKnn.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c HD.cpp -o HD.o

HD.cpp:25:14: warning: unused variable 'eps_Cmb1' [-Wunused-const-variable]

const double eps_Cmb1 = 1e-8;

             ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Knn.cpp -o Knn.o

Knn.cpp:146:15: warning: unused variable 'd' [-Wunused-variable]

        unsigned int d = points[0].size();unsigned int n = points.size();

                     ^

Knn.cpp:209:15: warning: unused variable 'd' [-Wunused-variable]

        unsigned int d = points[0].size();

                     ^

2 warnings generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Mahalanobis.cpp -o Mahalanobis.o

Mahalanobis.cpp:32:6: warning: unused variable 'res' [-Wunused-variable]

        int res = lu_factorize(A, pm);

            ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c OjaDepth.cpp -o OjaDepth.o

OjaDepth.cpp:44:8: warning: unused variable 'sc' [-Wunused-variable]

                bool sc = numSimplicesChecked == div0;

                     ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Polynomial.cpp -o Polynomial.o

Polynomial.cpp:396:18: warning: unused variable 'tmp' [-Wunused-variable]

        for (int i = 0, tmp; i < numPoints; i++){ input2[i][0] = input[i][1]; input2[i][1] = input[i][0]; } // swap columns

                        ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c PotentialDepth.cpp -o PotentialDepth.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ProjectionDepth.cpp -o ProjectionDepth.o

ProjectionDepth.cpp:16:12: warning: unused function 'CompareAsc' [-Wunused-function]

static int CompareAsc(OrderRec x, OrderRec y)

           ^

ProjectionDepth.cpp:21:12: warning: unused function 'CompareDec' [-Wunused-function]

static int CompareDec(OrderRec x, OrderRec y)

           ^

2 warnings generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c SimplicialDepth.cpp -o SimplicialDepth.o

SimplicialDepth.cpp:46:8: warning: unused variable 'sc' [-Wunused-variable]

                bool sc = numSimplicesChecked == div0;

                     ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c TukeyDepth.cpp -o TukeyDepth.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ZonoidDepth.cpp -o ZonoidDepth.o

ZonoidDepth.cpp:63:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]

    if ( RowInverted[j] = z[j] < 0 ) {

         ~~~~~~~~~~~~~~~^~~~~~~~~~

ZonoidDepth.cpp:63:25: note: place parentheses around the assignment to silence this warning

    if ( RowInverted[j] = z[j] < 0 ) {

                        ^

         (                        )

ZonoidDepth.cpp:63:25: note: use '==' to turn this assignment into an equality comparison

    if ( RowInverted[j] = z[j] < 0 ) {

                        ^

                        ==

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c asa047.cpp -o asa047.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ddalpha.cpp -o ddalpha.o

gfortran   -fPIC  -g -O2  -c depth.fd.f -o depth.fd.o

make: gfortran: No such file or directory

make: *** [depth.fd.o] Error 1

ERROR: compilation failed for package ‘ddalpha’

* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ddalpha’

The downloaded source packages are in

‘/private/tmp/RtmpUg5Cs2/downloaded_packages’

Warning message:

In install.packages(c("ddalpha", "recipes")) :

  installation of package ‘ddalpha’ had non-zero exit status

> 

 I want to extract all the reads mapped at chr5: 200-6000. 

what may be the cause that ΔΔG value in I-mutant and iStable server different for same mutation, when the predictor for iStable is I-mutant?

I-mutant ΔΔG value is -2.12

iStable ΔΔG value is -1.47

I sometime got confused with Synteny and Collinearity terminology. I am still wondering about the major differences.