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// MIT License
//
// Copyright (c) 2018 degski
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is

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• https://www.pacb.com/smrt-science/smrt-resources/datasets/
• https://github.com/PacificBiosciences/DevNet/wiki/Datasets

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#creates a base image from condo
FROM continuumio/miniconda3
SHELL ["/bin/bash", "-c"]

COPY environment.yml .

#run environment
#RUN conda env create -f environment.yml

RUN conda init bash

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// To compile:
//   gcc -g -O2 example.c libminimap2.a -lz

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

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// a combination of inverse square root (see wiki) and inversion: https://bits.stephan-brumme.com/inverse.html
static inline float mg_sqrtf(float x)
{	
	union { float f; uint32_t i; } z = { x };
	z.i  = 0x5f3759df - (z.i >> 1);
	z.f *= (1.5f - (x * 0.5f * z.f * z.f));
	z.i = 0x7EEEEEEE - z.i;
	return z.f;
}

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gg:ksw2_ggd.c cli.c ksw2.h
	$(CC) -Wall -g -O2 -o $@ ksw2_ggd.c cli.c

clean:
	rm -fr *.o *.dSYM gg

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CREATE TABLE seq (
	checksum TEXT,
	ac TEXT, -- INSDC sequence accession, when available
	len INTEGER, -- could be of type "TEXT"; no need to implement "less than"
	seq TEXT,
	PRIMARY KEY (checksum) -- what about collisions?
);
CREATE INDEX seq_len ON seq (len)
CREATE INDEX seq_ac ON seq (ac) -- different checksums may have the same AC

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NA12878 DirectRNA reads were obtained [here][raw-data] (passed reads only) and aligned with [minimap2][minimap2] v2.5 against the no_alt_analysis_set of GRCh38 plus SIRV contigs. It took <1 wall-clock hour across 16 CPU cores with command-line options: -cx splice -k14 --cs -uf -N20 -t16. Alignments were converted to BED with the misc/splice2bed.js script from minimap2 and then converted to BigBed. Ribosome-related genes (RPL*, RPS*, EEF* and RPSA) were excluded to reduce the file size. The final BigBed is hosted [at OSF][osf-prj].

A UCSC custom track is configured with

track type=bigBed name=NA12878-DirectRNA.minimap2-2.5 useScore=1 visibility=4 itemRgb="On" bigDataUrl=https://files.osf.io/v1/resources/b5nm2/providers/osfstorage/5a2347599ad5a10272ed5739?action=download&version=1&direct

You can access this track with the [following link][direct-link]. A GMAP alignment track is temporarily available [here][gmap]. This track contains 1/4 of reads. GMAP is still running. It will take 4–5 wall-clock

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#include <stdio.h>

#define SIMD_SSE     0x1
#define SIMD_SSE2    0x2
#define SIMD_SSE3    0x4
#define SIMD_SSSE3   0x8
#define SIMD_SSE4_1  0x10
#define SIMD_SSE4_2  0x20
#define SIMD_AVX     0x40
#define SIMD_AVX2    0x80

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#include <unistd.h>
#include <assert.h>
#include <stdlib.h>
#include <stdio.h>
#include "kstring.h"
#include "sam.h"
#include "kbtree.h"

typedef struct {
	int pos, n, sum;