endrebak endrebak

	# Example for https://www.biostars.org/p/193145

	import pybedtools
	import pysam

	# Use an example BAM file included with pybedtools
	fn = pybedtools.example_filename('x.bam')
	bam = pysam.Samfile(fn, 'r')

	# Filter reads using pysam. Since all aspects of the SAM-format read

	(ns dt.core
	(:require [datascript.core :as d]))

	;; schema so nice
	(def schema {:maker/email {:db/unique :db.unique/identity}

	:car/model {:db/unique :db.unique/identity}
	:car/maker {:db/type :db.type/ref}
	:car/colors {:db/cardinality :db.cardinality/many}})

	%%file _chi2.c
	#include <Python.h>
	#include <numpy/arrayobject.h>
	#include "chi2.h"

	static char module_docstring[] =
	"This module provides an interface for calculating chi-squared using C.";
	static char chi2_docstring[] =
	"Calculate the chi-squared of some data given a model.";

	#include <stdio.h>
	#include <string.h>
	#include <stdlib.h>
	#include <htslib/sam.h>

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

	samFile *fp_in = hts_open(argv[1],"r"); //open bam file
	bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //read header
	bam1_t *aln = bam_init1(); //initialize an alignment

	(ns sql-like-join
	(:require [clojure.set :refer [difference
	intersection
	union]]))

	(defn inner-join
	[left-keys right-keys]
	(intersection (set left-keys) (set right-keys)))

	(defn outer-join

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