<commit_before>// Implementation (work in progress) of the resequencing analysis pipeline used
// to teach the introductory NGS bioinformatics analysis course at SciLifeLab
// as described on this page:
// http://uppnex.se/twiki/do/view/Courses/NgsIntro1502/ResequencingAnalysis.html
package main

import (
	"fmt"
	sp "github.com/scipipe/scipipe"
	plib "github.com/scipipe/scipipe/proclib"
)

const (
	fastq_base_url = "http://bioinfo.perdanauniversity.edu.my/tein4ngs/ngspractice/"
	fastq_file_pat = "%s.ILLUMINA.low_coverage.4p_%s.fq"
	ref_base_url   = "http://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/"
	ref_file       = "Homo_sapiens.GRCh37.75.dna.chromosome.17.fa"
	ref_file_gz    = "Homo_sapiens.GRCh37.75.dna.chromosome.17.fa.gz"
	vcf_base_url   = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/"
	vcf_file       = "ALL.chr17.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz"
)

var (
	individuals = []string{"NA06984", "NA12489"}
	samples     = []string{"1", "2"}
)

func main() {
	// Create ungzip command pattern for later use<commit_msg>Specify dependencies in resequencing workflow<commit_after>// Implementation (work in progress) of the resequencing analysis pipeline used
// to teach the introductory NGS bioinformatics analysis course at SciLifeLab
// as described on this page:
// http://uppnex.se/twiki/do/view/Courses/NgsIntro1502/ResequencingAnalysis.html
// Prerequisites:
// - Samtools
// - BWA
// - Picard
// - GATK
// Install all tools except GATK like this on X/L/K/Ubuntu:
// sudo apt-get install samtools bwa picard-tools
// (GATK needs to be downloaded and installed manually from www.broadinstitute.org/gatk)
package main

import (
	"fmt"

	sp "github.com/scipipe/scipipe"
	plib "github.com/scipipe/scipipe/proclib"
)

const (
	fastq_base_url = "http://bioinfo.perdanauniversity.edu.my/tein4ngs/ngspractice/"
	fastq_file_pat = "%s.ILLUMINA.low_coverage.4p_%s.fq"
	ref_base_url   = "http://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/"
	ref_file       = "Homo_sapiens.GRCh37.75.dna.chromosome.17.fa"
	ref_file_gz    = "Homo_sapiens.GRCh37.75.dna.chromosome.17.fa.gz"
	vcf_base_url   = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/"
	vcf_file       = "ALL.chr17.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz"
)

var (
	individuals = []string{"NA06984", "NA12489"}
	samples     = []string{"1", "2"}
)

func main() {
	// Create ungzip command pattern for later use
{'fraction_non_alphanumeric': 0.13138108428967155, 'fraction_numerical': 0.03957261574990107, 'mean_word_length': 4.159183673469387, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 1, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 1, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1441402', 'n_tokens_mistral': 1084, 'n_tokens_neox': 988, 'n_words': 165}