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library(SKAT)
set.seed(1)

hap.skat.null = function(formula, covs, ...){
    covs = read.delim(covs)
    assign("y", covs[[as.character(formula[[2]])]], envir = .GlobalEnv)
    m = SKAT_Null_Model(formula, data=covs, out_type="D")
    return(m)
}

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usage:

shuf.sh "bedtools cmd" "metric" $genome

where metric must accept the output from bedtools cmd and return a single numeric value.

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package main

import (
	"bufio"
	"compress/gzip"
	"container/heap"
	"fmt"
	"io"
	"os"
	"strconv"

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set -eo pipefail

REF=human_g1k_v37_decoy.fasta
VCF=Mills_and_1000G_gold_standard.indels.b37.vcf.gz
VCF=/usr/local/src/gemini/test/test.mult-alts.fb.vep.vcf.gz

java -Xmx4G -jar /usr/local/src/gatk/GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants --splitMultiallelics --trimAlleles \
    -R $REF \
    --variant $VCF -o gatk.norm.vcf

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"""
This will standardize input file genotype fields to have AD=REF,ALT1,ALT2 ... (a
la GTK).

For platypus:  --depth NR --alt-depth NV
    varscan:   --ref-depth RD --alt-depth AD
    samtools:  --ref-depth DP4 (untested)

"""
import argparse

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from bx.bbi import bigwig_file
from bx.bbi import bigbed_file
print bigwig_file
import time
from hashlib import md5

prefix = '/data/gemini/data/hg19_fitcons_fc-i6-0_V1-01'


print "before bw: 8.6 seconds"

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$ gemini de_novo --columns "chrom, start, end, ref, alt" test.de_novo.db --min-kindreds 1 --gt-pl-max 1000 | cols

chrom  start      end        ref  alt  gene    variant_id    family_id  family_members                                                     family_genotypes  affected_samples  family_count
chr10  48003991   48003992   C    T    ASAH2C  variant_id:2  2          2_dad(dad;unaffected),2_mom(mom;unaffected),2_kid(child;affected)  C/C,C/C,C/T       2_kid             2
chr10  48004991   48004992   C    T    ASAH2C  variant_id:3  3          3_dad(dad;unaffected),3_mom(mom;unaffected),3_kid(child;affected)  C/C,C/C,C/T       3_kid             2
chr10  135336655  135336656  G    A    SPRN    variant_id:4  2          2_dad(dad;unaffected),2_mom(mom;unaffected),2_kid(child;affected)  G/G,G/G,G/A       2_kid             2
chr10  135336655  135336656  G    A    SPRN    variant_id:4  1          1_dad(dad;unaffected),1_mom(mom;unaffected),1_kid(child;affected)  G/G,G/G,G/A       1_kid             2
chr10  135

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with-bcolz	time (seconds)	bcolz-time	md5sum	num_lines	filter
True	2.8	0.62	5281fecb8571cc7c8e832e5682e865bb	16778	(gt_phred_ll_homalt).(*).(==0).(all)
False	155.2	NA	5281fecb8571cc7c8e832e5682e865bb	16778	(gt_phred_ll_homalt).(*).(==0).(all)
True	3.1	0.74	b2b75c9a56e128410a0e19708f096e2f	16750	((gt_phred_ll_homalt).().(==0).(all)) and (gt_types).().(==HOM_ALT).(all)
False	212.8	NA	b2b75c9a56e128410a0e19708f096e2f	16750	((gt_phred_ll_homalt).().(==0).(all)) and (gt_types).().(==HOM_ALT).(all)
True	1.4	0.42	c4885f35d03bed862d1e9d0ece71bc7c	2367	(gt_depths.{dad} > 20 and gt_depths.{mom} > 20 and gt_depths.{kid} > 20) and (gt_types.{dad} == HOM_REF and gt_types.{mom} == HOM_REF and gt_types.{kid} != HOM_REF)
False	203.0	NA	c4885f35d03bed862d1e9d0ece71bc7c	2367	(gt_depths.{dad} > 20 and gt_depths.{mom} > 20 and gt_depths.{kid} > 20) and (gt_types.{dad} == HO

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diff --git a/src/extended/gff3_visitor.c b/src/extended/gff3_visitor.c
index 8246680..9e87612 100644
--- a/src/extended/gff3_visitor.c
+++ b/src/extended/gff3_visitor.c
@@ -197,32 +197,52 @@ static int store_ids(GtGenomeNode *gn, void *data, GtError *err)
   AddIDInfo add_id_info;
   int had_err = 0;
   GtStr *id;
+  /* Q: is this const ok? */
+  const char *idstring;

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diff --git a/src/extended/gff3_out_stream.c b/src/extended/gff3_out_stream.c
index 6dbbc23..f813e8f 100644
--- a/src/extended/gff3_out_stream.c
+++ b/src/extended/gff3_out_stream.c
@@ -18,6 +18,7 @@
 #include "extended/gff3_out_stream.h"
 #include "extended/gff3_visitor.h"
 #include "extended/node_stream_rep.h"
+#include "core/cstr_table.h"