malonge

#!/usr/bin/python3
import argparse
from collections import defaultdict

"""
This utility converts a SAM file to a nucmer delta file.

SAM files must contain an NM tag, which is default in minimap2 alignments.  
"""

lh3

/*
  For any 1<k<=64, let mask=(1<<k)-1. hash_64() is a bijection on [0,1<<k), which means
  hash_64(x, mask)==hash_64(y, mask) if and only if x==y. hash_64i() is the inversion of
  hash_64(): hash_64i(hash_64(x, mask), mask) == hash_64(hash_64i(x, mask), mask) == x.
*/

// Thomas Wang's integer hash functions. See <https://gist.github.com/lh3/59882d6b96166dfc3d8d> for a snapshot.
uint64_t hash_64(uint64_t key, uint64_t mask)
{
	key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;

l-modolo

#!/bin/sh
# compute reads length distribution from a fastq file
awk 'NR%4 == 2 {lengths[length($0)]++} END {for (l in lengths) {print l, lengths[l]}}'  file.fastq

epinna

#                                                                                                        
#   STL GDB evaluators/views/utilities - 1.03
#
#   The new GDB commands:                                                         
# 	    are entirely non instrumental                                             
# 	    do not depend on any "inline"(s) - e.g. size(), [], etc
#       are extremely tolerant to debugger settings
#                                                                                 
#   This file should be "included" in .gdbinit as following:
#   source stl-views.gdb or just paste it into your .gdbinit file

donny-dont

#ifdef _WIN32
#include <malloc.h>
#endif
#include <cstdint>
#include <vector>
#include <iostream>

/**
 * Allocator for aligned data.