bioinfornatics

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bioinfornatics

#!/usrbin/env python

def getMaxRowLength( matrix ):
    maxLen = 0
    for i in matrix:
        if len(i) > maxLen:
            maxLen = len(i)
    return maxLen

def computeDiag( matrix, i , j ):

bioinfornatics

#!/usr/bin/env perl
use strict;
use warnings;
use 5.010;
use List::MoreUtils qw(uniq);
#use Data::Dumper::Names;
use Benchmark qw(:all) ;

sub test1 {
  my @tab = (["12","25","2","18","9","25","18","30","30","12","30","30","18","12"],["154","12","56","8","22","88","74","12","56","32","88","88","56","12","12","56"]);

bioinfornatics

#!/usr/bin/env perl
use strict;
use warnings;
use 5.010;
use List::MoreUtils qw(uniq);
use Data::Dumper::Names;

my @tab = (["12","25","2","18","9","25","18","30","30","12","30","30","18","12"],["154","12","56","8","22","88","74","12","56","32","88","88","56","12","12","56"]);

print "=============Before=============\n";

bioinfornatics

$ diff runtime/phobos/std/regex.d ../phobos/std/regex.d
184c184
<     $(WEB http://unicode.org/reports/tr18/, UTS 18). Specifically:
---
>     $(WEB unicode.org/reports/tr18/, UTS 18). Specifically:
5560a5561,5564
>         static if(direction == OneShot.Fwd)
>             startPc = startPc;
>         else
>             startPc = cast(uint)re.ir.length-IRL!(IR.LookbehindEnd);

bioinfornatics

import std.string;
import std.stdio;
import std.range;
import std.lowercase;


mixin template delegates( alias instance, methods... ){
    static if( methods.length > 0 ){
            static if( hasmembers(instance, methods[0]) ){
                alias ReturnType!(methods[0]) type;                 // function/method type returned for first method

bioinfornatics

import std.traits;
import std.stdio;
import std.string;
import std.range;
import std.ascii; // lowercase

static string getFunctionParameterString(T, S)( T ptt, S pstc ) @safe pure nothrow{
    enum result = "";
    static if(  ptt.length > 0 && pstc.length > 0 && ptt.length == pstc.length){
        result = ptt[0].stringof ~" "~ pstc.stringof ~" ";

bioinfornatics

import std.string;
import std.stdio;
import std.range;

mixin template arrayDelegator( alias instance, methods... ){
   static if( methods.length > 0 ){
        static if( methods[0] == "opIndexAssign" ){
            mixin("
    void opIndexAssign( " ~ ElementEncodingType!(typeof(instance)).stringof ~ " value, size_t index ){ 
        array[index] = value;

bioinfornatics

/**
 * The module csv is a set of function to parse many format using a delimitter as csv file
 * Supported format:
 *  - .mat matrix file
 *  - .bed UCSC file
 * For parse a .csv file use std.csv
 */
module bed;

import std.conv;

bioinfornatics

/**
 * The module csv is a set of function to parse many format using a delimitter as csv file
 * Supported format:
 *  - .mat matrix file
 *  - .bed UCSC file
 * For parse a .csv file use std.csv
 */
module bed;

import std.conv;