Added test files

tests/get-timings.pl

@@ -0,0 +1,40 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $time = "wall clock";
+my $mem = "Maximum resident set size";
+my $sep = ";";
+
+sub uutime {
+		my $wt_h = `grep '$time' $_[0] | sed 's/.* //'`; chomp $wt_h;
+		return $wt_h;
+}
+
+my $K="kraken";
+
+print join($sep,qw/sample mbpm1 mbpm2 time1 time2 time3 mem1 mem2/),"\n";
+for my $hll_t (@ARGV) {
+		my $bn = `basename $hll_t .krakenhll.timing.log`; chomp $bn;
+		die "$hll_t should be an hll timing log" if $bn == $hll_t;
+		print "$bn$sep";
+		(my $hll = $hll_t) =~ s/.timing//;
+		(my $k = $hll) =~ s/krakenhll/$K/;
+		(my $k_t = $hll_t) =~ s/krakenhll/$K/;
+		(my $kr_t = $hll_t) =~ s/krakenhll/$K-report/;
+
+		my $hm = `grep -o '[0-9\.]* Mbp/m' $hll | sed 's/ .*//'`; chomp $hm;
+		print $hm,$sep;
+		my $km = `grep -o '[0-9\.]* Mbp/m' $k | sed 's/ .*//'`; chomp $km;
+		print $km,$sep;
+
+		print uutime($hll_t),$sep;
+		print uutime($k_t),$sep;
+		print uutime($kr_t),$sep;
+
+		my $mem_h = `grep '$mem' $hll_t | sed 's/.* //'`; chomp $mem_h;
+		print $mem_h,$sep;
+		my $mem_k = `grep '$mem' $k_t | sed 's/.* //'`; chomp $mem_k;
+		print $mem_k,"\n";
+}

tests/run-fq.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+
+TIME="/usr/bin/time -v"
+FILES=/ccb/salz4-1/fbreitwieser/microbiome-pipeline/staging/CP_PT{[0-9],10}-*.fastq.gz
+
+for J in 1 2; do
+	for THREADS in 10 5 2 1; do 
+
+		krakenhll --preload --db ../dbs/refseq-oct2017-k31 --report-file /dev/null --fasta <(printf ">A\nA")
+		for B in $*; do 
+			echo $B
+			BN=`basename $B .fastq.gz` && echo $BN && BN="$BN.t$THREADS.j$J" 
+			$TIME -o log/$BN.krakenhll.timing.log krakenhll --db ../dbs/refseq-oct2017-k31 --fastq --gzip --report-file report/$BN.krakenhll.report --threads $THREADS $B > kraken/$BN.krakenhll.kraken 2> log/$BN.krakenhll.log; 
+		done
+
+		kraken --preload --db ../dbs/refseq-oct2017-k31 --fasta <(printf ">A\nA")
+		for B in $*; do 
+			echo $B
+			BN=`basename $B .fastq.gz` && echo $BN && BN="$BN.t$THREADS.j$J" 
+			$TIME -o log/$BN.kraken.timing.log kraken --db ../dbs/refseq-oct2017-k31 --fastq --gzip  --threads $THREADS $B > kraken/$BN.kraken 2> log/$BN.kraken.log
+			$TIME -o log/$BN.kraken-report.timing.log kraken-report --db ../dbs/refseq-oct2017-k31 kraken/$BN.kraken > report/$BN.kraken.report; 
+		done
+
+	done
+done
+