In this exercise we are going to download human genomic data generated by the New York Genome Center (NYGC). Information about the data can be found here and details about their pipeline can be found here.
We will start by setting up a git repository on the cluster to hold our project data.
$ mkdir brca1-project
$ cd brca1-project
$ git init
Today we will be working with data from the National Health and Nutrition Examination Survey (NHANES).
NHANES is a program of studies designed to assess the health and nutritional status of adults and children in the United States. The survey is unique in that it combines interviews and physical examinations. NHANES is a major program of the National Center for Health Statistics (NCHS). NCHS is part of
| /* | |
| This file contains examples of how to do full-width 32-bit multiplication by dividing each | |
| operand into 16-bit fields. | |
| */ | |
| typedef struct { | |
| int low; | |
| int high; | |
| } int_pair_t; | |
| ##gff-version 3 | |
| #!gff-spec-version 1.21 | |
| #!processor NCBI annotwriter | |
| #!genome-build ASM1798v1 | |
| #!genome-build-accession NCBI_Assembly:GCF_000017985.1 | |
| #!annotation-date 06/08/2024 00:48:35 | |
| #!annotation-source NCBI RefSeq GCF_000017985.1-RS_2024_06_08 | |
| ##sequence-region NC_012967.1 1 4629812 | |
| ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=413997 | |
| NC_012967.1 RefSeq region 1 4629812 . + . ID=NC_012967.1:1..4629812;Dbxref=taxon:413997;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=REL606 |
| // Copyright 2021 Johan Rade (johan.rade@gmail.com) | |
| // Distributed under the MIT license (https://opensource.org/licenses/MIT) | |
| #ifndef FAST_EXP_H | |
| #define FAST_EXP_H | |
| #include <cstdint> | |
| #include <cstring> | |