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ppxh-gr's Introduction

👋 Hi there, I'm Yuri Pirola

🎓 I'm an associate professor at DISCo, University of Milano-Bicocca (Milan) working on computational problems arising from 📈 large quantities of data now available in Bioinformatics.

🌱 My main interests involve the study of the computational complexity of optimization problems, the design of exact/approximation/parameterized algorithms for their resolution, and their implementation and experimentation.

⬇️ Check my repos and the repos I contribute to if you are curious to see what I'am working on.

🔎 Do you want more details? Check my CV (or its extended version)!

📫 How to reach me? Dropping me an e-mail ([email protected]) is the easiest and fastest way.

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ppxh-gr's Issues

Compilation failed on Ubuntu 11.10

The compilation of the software (make all) fails with the following error:

Compiling src/abort.c
Compiling src/bit_matrix.c
Compiling src/bit_vector.c
Compiling src/my_time.c
Compiling src/rnd.c
Compiling src/util.c
Compiling src/heuristic.c
src/heuristic.c: In function ‘execute_GR’:
src/heuristic.c:332:7: warning: unused variable ‘exit_result’ [-Wunused-variable]
 * Linking bin/ppxh-gr
obj/rnd.o: In function `RG_create':
.../src/rnd.c:43: undefined reference to `gsl_rng_mt19937'
.../src/rnd.c:43: undefined reference to `gsl_rng_alloc'
.../src/rnd.c:45: undefined reference to `gsl_rng_set'
.../src/rnd.c:46: undefined reference to `gsl_rng_set'
obj/rnd.o: In function `RG_create_seed':
.../src/rnd.c:54: undefined reference to `gsl_rng_mt19937'
.../src/rnd.c:54: undefined reference to `gsl_rng_alloc'
.../src/rnd.c:56: undefined reference to `gsl_rng_set'
obj/rnd.o: In function `RG_destroy':
.../src/rnd.c:64: undefined reference to `gsl_rng_free'
obj/rnd.o: In function `RG_next_int_between':
.../src/rnd.c:89: undefined reference to `gsl_rng_uniform_int'
obj/rnd.o: In function `RG_next_bool':
.../src/rnd.c:96: undefined reference to `gsl_rng_uniform_int'
obj/rnd.o: In function `RG_next_int':
.../src/rnd.c:72: undefined reference to `gsl_rng_get'
obj/rnd.o: In function `RG_next_int_less_than':
.../src/rnd.c:81: undefined reference to `gsl_rng_uniform_int'
obj/rnd.o: In function `RG_next_probability':
.../src/rnd.c:103: undefined reference to `gsl_rng_uniform'
collect2: ld returned 1 exit status
make: *** [heu] Error 1

System: Ubuntu 11.10
PPXH-GR version: v1.0.0

Enhancement proposal: explicitly provides the haplotype resolutions of the xor-genotypes

The program prints only the final haplotype matrix without providing, for each xor-genotype in input, the pair of haplotypes which solves it.
Such information is instead useful and should be provided.

For example, given the genotype matrix:

g0:  10
g1:  01
g2:  11

And given a computed solution (haplotype matrix):

h0:  00
h1:  10
h2:  01

It would be useful to know that the first genotype (g0) is solved by haplotypes h0 and h1, genotype g1 is solved by h0 and h2, and genotype g2 is solved by h1 and h2.

PPXH-GR version: v1.0.0

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