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#include <zlib.h>
#include <stdint.h>
#include <unistd.h>
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <math.h>

#include "kseq.h"

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#!/usr/bin/env perl

use strict;
use warnings;

die("Usage: gem2sam.pl <gem.map>\n") if (@ARGV == 0 && -t STDIN);

while (<>) {
	chomp;
	my @t = split("\t");

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var getopt = function(args, ostr) {
  var oli; // option letter list index
	if (typeof(getopt.place) == 'undefined')
		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
	if (getopt.place == -1) { // update scanning pointer
		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
			getopt.place = -1;
			return null;
		}
		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"

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#!/usr/bin/env perl

use strict;
use warnings;

&main;

sub main {
	my $last = '';
	my @lines;

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>670363126:1315126374:97-3576:131-3480:1-3350 no hit?!
TTGAACAAGTTCAATTTAAAATATTTCATAAGCTTGTATGATATCATTGGGGCTAGAGTAGACGTGATACTAAATGTAGGAAATAAATGGAATAAACACTCAGAGAGGAACTATATGTTTTGTCTTAAAACTTCATTAAGTCTAAGAATTGATATTTTGTTGCTGGATGAATTGGTGGTTTGTGAGTTATAGTGAATATATCTCCCTGTTACATTCCTGTCGTTGTCCTATCCATTGTCCTATTGTTGGATGTTTCACTTGTGTATCCCATGTTACATAATTTTATCATAGAGAGCAAAAGAATTTGACTACAGTAAACTTAATGCTTTGCCATGTACAGATGTATGACAAAGAACATGTTATTTTGAAAGTTTTTGCTCTTATATTTTCTTTGCAGTCTGACTTCTTAATATTTGCTTCATTTTCATGTATGTGTTTTTACAAAGCATTCTCTTGGTATCACTAACCAAATACCTGTTTAGAGAAACAAAAGGCCAACTGGGGATGAAAACAGTTTATTTACTTACTGCACAGTATGTTTCTAGCTCTCTGTTATAAGAACAACAGTGTATTTGGTGTGTGTGTAGAACATACTTATTAAAAGTTTGATTCCTCTTTCCCCCGCAGATTCCATGATGAAGCCTTGTGATTTTGTGTCTTTACAAACTGTTCACTGATCTGGCAATGAAAATTGCCTCGATGTTAATAAATATTAGTTCATTAGCTATGCTTAATTAACACAAATGAAACTGATGAACCCAGTGTTGTGTGTTATTGCAAGCTTTCTATTTATATCAGCAAACCTCAGCGTTTATGATTTATTAAATAATTTATTCAATAGGCATTAATTGAGTATCAAGTATCAGTCAGAGACTTTGCTAAATGTTGCAAACCCAAATATGTCTTAAAGGAGTATACTGTCTTTCAAAAAATAGATGGCTAAAAAATAGTTATAATATAGATGATATA

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// gcc -g -O2 -Wall fmr-rld.c mrope.c rle.c rope.c rld0.c -o fmr-rld -pthread

#include <stdio.h>
#include <stdint.h>
#include "rle.h"
#include "rld0.h"
#include "mrope.h"

int main(int argc, char *argv[])
{

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#include <zlib.h>
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)

unsigned char seq_nt6_table[256] = {
    0, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,

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References:

• https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader
• https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference

Steps:

1. Follow steps 1-5 in the first link above to acquire access_token. This will take a while, but you only need to do this once. Never share this token!!
2. Find the file you want to download. Copy the link, which looks something like: https://basespace.illumina.com/sample/9804795/files/tree/NA12878-L1_S1_L001_R1_001.fastq.gz?id=515013503. The "id" is the unique file identifier.
3. Download the file with: wget -O filename 'https://api.basespace.illumina.com/v1pre3/files/{id}/content?access_token={token}', where {token} is from step 1 and {id} from step 2.

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# generate the list of novel segments for each sample
seqtk seq -L200 001*.mag.gz | ./fermi2 match -dk101 hs38a.fmd /dev/stdin | k8 hs38d.js fm2seg -p 001 | gzip > 001.novel.gz
k8 hs38d.js tab2fa 001.novel.gz | bwa-r868 mem s38a.fa - | k8 hs38d.js dropsim | gzip -1 > 001.dropped.gz
tabtk isct -c 001.dropped.gz 001.novel.gz | gzip -1 > 001.div1.gz

#
zcat div1/*.div1.gz | cut -f1-5 | sort -k5,5 -k1,1 -S60G | k8 hs38d.js fixname | gzip -1 > 01ori.txt.gz
# tabtk isct -c gbk.novel.dropped gbk.novel.gz | sort -k5,5 -k1,1 -S60G | grep -v NNNNNNNNNN | gzip -1 > 01ori.txt.gz
tabtk isct -d_ -c contaminated.txt 01ori.txt.gz | gzip -1 > 02contam.txt.gz
# zcat 01ori.txt.gz|grep -vFf DoNotUseList_May2011.list | gzip -1 > 02contam.txt.gz

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\documentclass[pdftex,10pt]{article}

\usepackage{amsmath}
\usepackage{amssymb}

\title{PCR and mapping duplicate rate in NGS}
\author{Heng Li}

\begin{document}