diff --git a/CHANGELOG b/CHANGELOG
new file mode 100644
index 0000000..d9e5fb7
--- /dev/null
+++ b/CHANGELOG
@@ -0,0 +1,52 @@
+v0.10.3-beta:
+* remove Fatal.pm use in kraken-report
+* fixed false success message on make failure in installer
+* explicitly require g++ as C++ compiler in Makefile
+* change to quickfile.cpp to do proper syncing on close
+* fixed kraken-build bug w/ --work-on-disk (cause of some major build stalls)
+* changed hash size calculation to use Perl
+* close input files explicitly in db_sort/db_shrink to reduce reported memory
+* allow db_shrink to work in RAM
+* updates to README file
+
+v0.10.2-beta:
+* fixed kraken-report bug w/ --show-zeros
+* fixed kraken-report installation bug
+* updates to README file
+
+v0.10.1-beta:
+* fixed 2nd bug in build_kraken.sh in calculating hash size (thanks T. Antao)
+* fixed bug in add_to_library.sh for some bash versions (thanks T. Antao)
+* fixed issue where search window wasn't cached until a failure (query speedup)
+* added $KRAKEN_DIR fallback for kraken/kraken-build (thanks S. Koren)
+
+v0.10.0-beta:
+* added CHANGELOG
+* fixed quick mode hit list output
+* updated README citation
+* changed minimizer sort order (query speedup), changes database structure
+* use linear search with small windows (query speedup)
+* changed query procedure (query speedup); search w/o 1st calculating minimizer
+* changed readlink in installer to perl Cwd::abs_path (portability)
+* removed MAP_POPULATE for preloading, uses read loop instead (bugfix/port.)
+* added --work-on-disk switch to kraken-build
+* added kraken-report script
+* fixed bug in build_kraken.sh in calculating hash size (thanks T. Antao)
+
+v0.9.1b:
+* fixed bug to allow kraken-build --shrink
+
+v0.9.0b:
+* full rewrite
+* minimizers used to speed queries, prefix index removed
+
+v0.3:
+* DB build parallelized, Jellyfish removed from LCA assignment
+
+v0.2:
+* full rewrite, most progs. changed to C++
+* Jellyfish removed from classification step
+* prefix index used to speed queries
+
+v0.1:
+* initial version, mostly Perl
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,674 @@
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+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ Copyright (C)
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+.
diff --git a/install_kraken.sh b/install_kraken.sh
new file mode 100755
index 0000000..8e0674f
--- /dev/null
+++ b/install_kraken.sh
@@ -0,0 +1,61 @@
+#!/bin/bash
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+set -e
+
+VERSION="0.10.3-beta"
+
+if [ -z "$1" ] || [ -n "$2" ]
+then
+ echo "Usage: $(basename $0) KRAKEN_DIR"
+ exit 64
+fi
+
+if [ "$1" = "KRAKEN_DIR" ]
+then
+ echo "Please replace \"KRAKEN_DIR\" with the name of the directory"
+ echo "that you want to install Kraken in."
+ exit 1
+fi
+
+# Perl cmd used to canonicalize dirname - "readlink -f" doesn't work
+# on OS X.
+export KRAKEN_DIR=$(perl -MCwd=abs_path -le 'print abs_path(shift)' "$1")
+
+(cd src && make)
+mkdir -p "$KRAKEN_DIR"
+for file in scripts/*.broken
+do
+ perl -pl -e 'BEGIN { while (@ARGV) { $_ = shift; ($k,$v) = split /=/, $_, 2; $H{$k} = $v } }'\
+ -e 's/#####=(\w+)=#####/$H{$1}/g' \
+ "KRAKEN_DIR=$KRAKEN_DIR" "VERSION=$VERSION" \
+ < "$file" > "$KRAKEN_DIR/$(basename $file .broken)"
+done
+cp scripts/*.sh "$KRAKEN_DIR"
+make -C src install
+chmod -R +x "$KRAKEN_DIR"
+
+echo
+echo "Kraken installation complete."
+echo
+echo "To make things easier for you, you may want to copy/symlink the following"
+echo "files into a directory in your PATH:"
+echo " $KRAKEN_DIR/kraken"
+echo " $KRAKEN_DIR/kraken-build"
+echo " $KRAKEN_DIR/kraken-report"
diff --git a/scripts/add_to_library.sh b/scripts/add_to_library.sh
new file mode 100755
index 0000000..fa25dc6
--- /dev/null
+++ b/scripts/add_to_library.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+# Copy specified file into a Kraken library
+
+set -u # Protect against uninitialized vars.
+set -e # Stop on error
+
+LIBRARY_DIR="$KRAKEN_DB_NAME/library"
+
+if [ ! -e "$1" ]
+then
+ echo "Can't add \"$1\": file does not exist"
+ exit 1
+fi
+if [ ! -f "$1" ]
+then
+ echo "Can't add \"$1\": not a regular file"
+ exit 1
+fi
+
+if ! head -1 "$1" | perl -nle 'exit 1 unless /^>gi\|(\d+)\|/'
+then
+ echo "Can't add \"$1\": could not find GI number"
+ exit 1
+fi
+seq_ct=$(grep -m2 '^>' "$1" | wc -l)
+if (( seq_ct > 1 ))
+then
+ echo "Can't add \"$1\": multiple sequences found"
+ exit 1
+fi
+
+mkdir -p "$LIBRARY_DIR/added"
+ct=0
+freefile=""
+while [ -z "$freefile" ]
+do
+ freefile=$(seq -f '%015g' $ct $ct).fna
+ if [ -e "$LIBRARY_DIR/added/$freefile" ]
+ then
+ ct=$(($ct + 1))
+ freefile=""
+ fi
+done
+cp "$1" "$LIBRARY_DIR/added/$freefile"
+echo "Added \"$1\" to library ($KRAKEN_DB_NAME)"
diff --git a/scripts/build_kraken_db.sh b/scripts/build_kraken_db.sh
new file mode 100755
index 0000000..c9a29dd
--- /dev/null
+++ b/scripts/build_kraken_db.sh
@@ -0,0 +1,186 @@
+#!/bin/bash
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+# Build a Kraken database
+# Designed to be called by kraken_build
+
+set -u # Protect against uninitialized vars.
+set -e # Stop on error
+set -o pipefail # Stop on failures in non-final pipeline commands
+
+function report_time_elapsed() {
+ curr_time=$(date "+%s.%N")
+ perl -e '$time = $ARGV[1] - $ARGV[0];' \
+ -e '$sec = int($time); $nsec = $time - $sec;' \
+ -e '$min = int($sec/60); $sec %= 60;' \
+ -e '$hr = int($min/60); $min %= 60;' \
+ -e 'print "${hr}h" if $hr;' \
+ -e 'print "${min}m" if $min || $hr;' \
+ -e 'printf "%.3fs", $sec + $nsec;' \
+ $1 $curr_time
+}
+
+start_time=$(date "+%s.%N")
+
+DATABASE_DIR="$KRAKEN_DB_NAME"
+
+if [ ! -d "$DATABASE_DIR" ]
+then
+ echo "Can't find Kraken DB directory \"$KRAKEN_DB_NAME\""
+ exit 1
+fi
+cd "$DATABASE_DIR"
+
+MEMFLAG=""
+if [ -z "$KRAKEN_WORK_ON_DISK" ]
+then
+ MEMFLAG="-M"
+ echo "Kraken build set to minimize disk writes."
+else
+ echo "Kraken build set to minimize RAM usage."
+fi
+
+if [ -e "database.jdb" ]
+then
+ echo "Skipping step 1, k-mer set already exists."
+else
+ echo "Creating k-mer set (step 1 of 6)..."
+ start_time1=$(date "+%s.%N")
+
+ # Estimate hash size as 1.15 * chars in library FASTA files
+ if [ -z "$KRAKEN_HASH_SIZE" ]
+ then
+ KRAKEN_HASH_SIZE=$(find library/ -name '*.fna' -printf '%s\n' | perl -nle '$sum += $_; END {printf "%d\n", 1.15 * $sum}')
+ echo "Hash size not specified, using '$KRAKEN_HASH_SIZE'"
+ fi
+
+ find library/ -name '*.fna' -print0 | xargs -0 cat | \
+ jellyfish count -m $KRAKEN_KMER_LEN -s $KRAKEN_HASH_SIZE -C -t $KRAKEN_THREAD_CT \
+ -o database /dev/fd/0
+
+ # Merge only if necessary
+ if [ -e "database_1" ]
+ then
+ jellyfish merge -o database.jdb.tmp database_*
+ else
+ mv database_0 database.jdb.tmp
+ fi
+
+ # Once here, DB is finalized, can put file in place.
+ mv database.jdb.tmp database.jdb
+
+ echo "K-mer set created. [$(report_time_elapsed $start_time1)]"
+fi
+
+if [ -z "$KRAKEN_MAX_DB_SIZE" ]
+then
+ echo "Skipping step 2, no database reduction requested."
+else
+ if [ -e "database.jdb.big" ]
+ then
+ echo "Skipping step 2, database reduction already done."
+ else
+ start_time1=$(date "+%s.%N")
+ kdb_size=$(stat -c '%s' database.jdb)
+ idx_size=$(echo "8 * (4 ^ $KRAKEN_MINIMIZER_LEN + 2)" | bc)
+ resize_needed=$(echo "scale = 10; ($kdb_size+$idx_size)/(2^30) > $KRAKEN_MAX_DB_SIZE" | bc)
+ if (( resize_needed == 0 ))
+ then
+ echo "Skipping step 2, database reduction unnecessary."
+ else
+ echo "Reducing database size (step 2 of 6)..."
+ max_kdb_size=$(echo "$KRAKEN_MAX_DB_SIZE*2^30 - $idx_size" | bc)
+ if (( $(echo "$max_kdb_size < 0" | bc) == 1 ))
+ then
+ echo "Maximum database size too small, aborting reduction."
+ exit 1
+ fi
+ # Key ct is 8 byte int stored 48 bytes from start of file
+ key_ct=$(perl -MFcntl -le 'open F, "database.jdb"; seek F, 48, SEEK_SET; read F, $b, 8; $a = unpack("Q", $b); print $a')
+ overage=$(echo "($kdb_size - $max_kdb_size + 11) / 12" | bc)
+ percentage=$(echo "100 * ($key_ct - $overage) / $key_ct" | bc)
+ echo "Using $percentage percent of original database."
+ db_shrink $MEMFLAG -d database.jdb -o database.jdb.small -p $percentage
+ mv database.jdb database.jdb.big.tmp
+ mv database.jdb.small database.jdb
+ mv database.jdb.big.tmp database.jdb.big
+ echo "Database reduced. [$(report_time_elapsed $start_time1)]"
+ fi
+ fi
+fi
+
+if [ -e "database.kdb" ]
+then
+ echo "Skipping step 3, k-mer set already sorted."
+else
+ echo "Sorting k-mer set (step 3 of 6)..."
+ start_time1=$(date "+%s.%N")
+ db_sort -z $MEMFLAG -t $KRAKEN_THREAD_CT -n $KRAKEN_MINIMIZER_LEN \
+ -d database.jdb -o database.kdb.tmp \
+ -i database.idx
+
+ # Once here, DB is sorted, can put file in proper place.
+ mv database.kdb.tmp database.kdb
+
+ echo "K-mer set sorted. [$(report_time_elapsed $start_time1)]"
+fi
+
+if [ -e "gi2file.map" ]
+then
+ echo "Skipping step 4, GI number to file map already complete."
+else
+ echo "Creating GI number to file map (step 4 of 6)..."
+ start_time1=$(date "+%s.%N")
+ find library/ -name '*.fna' -print0 | \
+ xargs -0 grep -m1 -H '^>' | \
+ awk -F '\\|' '{ sub(/:>gi$/, "", $1); print $2 "|" $1 }' \
+ > gi2file.map.tmp
+ mv gi2file.map.tmp gi2file.map
+
+ echo "GI number to file map created. [$(report_time_elapsed $start_time1)]"
+fi
+
+if [ -e "file2taxon.map" ]
+then
+ echo "Skipping step 5, file to taxon map already complete."
+else
+ echo "Creating file to taxon map (step 5 of 6)..."
+ start_time1=$(date "+%s.%N")
+ make_file_to_taxon_map taxonomy/gi_taxid_nucl.dmp gi2file.map \
+ > file2taxon.map.tmp
+ mv file2taxon.map.tmp file2taxon.map
+ line_ct=$(wc -l file2taxon.map | awk '{print $1}')
+
+ echo "$line_ct files mapped to taxa. [$(report_time_elapsed $start_time1)]"
+fi
+
+if [ -e "lca.complete" ]
+then
+ echo "Skipping step 6, LCAs already set."
+else
+ echo "Setting LCAs in database (step 6 of 6)..."
+ start_time1=$(date "+%s.%N")
+ set_lcas $MEMFLAG -x -d database.kdb -i database.idx \
+ -n taxonomy/nodes.dmp -t $KRAKEN_THREAD_CT -f file2taxon.map
+ touch "lca.complete"
+
+ echo "Database LCAs set. [$(report_time_elapsed $start_time1)]"
+fi
+
+echo "Database construction complete. [Total: $(report_time_elapsed $start_time)]"
diff --git a/scripts/clean_db.sh b/scripts/clean_db.sh
new file mode 100755
index 0000000..84bf208
--- /dev/null
+++ b/scripts/clean_db.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+# Clean unneeded files from a database
+
+set -u # Protect against uninitialized vars.
+set -e # Stop on error
+
+cd "$KRAKEN_DB_NAME"
+
+[ -e "database.kdb" ] || (echo "Incomplete database, clean aborted."; exit 1)
+[ -e "database.idx" ] || (echo "Incomplete database, clean aborted."; exit 1)
+[ -e "taxonomy/nodes.dmp" ] || (echo "Incomplete database, clean aborted."; exit 1)
+[ -e "taxonomy/names.dmp" ] || (echo "Incomplete database, clean aborted."; exit 1)
+
+rm -rf library
+rm -f database.jdb* database_* *.map lca.complete
+mkdir newtaxo
+mv taxonomy/{nodes,names}.dmp newtaxo
+rm -rf taxonomy
+mv newtaxo taxonomy
diff --git a/scripts/download_genomic_library.sh b/scripts/download_genomic_library.sh
new file mode 100755
index 0000000..d567b22
--- /dev/null
+++ b/scripts/download_genomic_library.sh
@@ -0,0 +1,95 @@
+#!/bin/bash
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+# Download specific genomic libraries for use with Kraken.
+# Supported choices are:
+# bacteria - NCBI RefSeq complete bacterial/archaeal genomes
+# viruses - NCBI RefSeq complete viral genomes
+# human - NCBI RefSeq GRCh37 human reference genome
+
+set -u # Protect against uninitialized vars.
+set -e # Stop on error
+
+LIBRARY_DIR="$KRAKEN_DB_NAME/library"
+NCBI_SERVER="ftp.ncbi.nih.gov"
+FTP_SERVER="ftp://$NCBI_SERVER"
+RSYNC_SERVER="rsync://$NCBI_SERVER"
+THIS_DIR=$PWD
+
+case "$1" in
+ "bacteria")
+ mkdir -p $LIBRARY_DIR/Bacteria
+ cd $LIBRARY_DIR/Bacteria
+ if [ ! -e "lib.complete" ]
+ then
+ rm -f all.fna.tar.gz
+ wget $FTP_SERVER/genomes/Bacteria/all.fna.tar.gz
+ echo -n "Unpacking..."
+ tar zxf all.fna.tar.gz
+ rm all.fna.tar.gz
+ echo " complete."
+ touch "lib.complete"
+ else
+ echo "Skipping download of bacterial genomes, already downloaded here."
+ fi
+ ;;
+ "viruses")
+ mkdir -p $LIBRARY_DIR/Viruses
+ cd $LIBRARY_DIR/Viruses
+ if [ ! -e "lib.complete" ]
+ then
+ rm -f all.fna.tar.gz
+ wget $FTP_SERVER/genomes/Viruses/all.fna.tar.gz
+ echo -n "Unpacking..."
+ tar zxf all.fna.tar.gz
+ rm all.fna.tar.gz
+ echo " complete."
+ touch "lib.complete"
+ else
+ echo "Skipping download of viral genomes, already downloaded here."
+ fi
+ ;;
+ "human")
+ if [ ! -e "$LIBRARY_DIR/H_sapiens/lib.complete" ]
+ then
+ rsync -avz --include "H_sapiens/" --include "*/CHR_*/" --include "hs_ref_GRCh37*.fa.gz" --exclude "*" \
+ $RSYNC_SERVER/genomes/H_sapiens $LIBRARY_DIR
+ for gzfile in $LIBRARY_DIR/H_sapiens/*/*.gz
+ do
+ dir=$(dirname $gzfile)
+ cd $dir
+ gunzip $(basename $gzfile)
+ echo "Unzipped $(basename $gzfile)"
+ cd $THIS_DIR
+ done
+ for fafile in $LIBRARY_DIR/H_sapiens/*/*.fa
+ do
+ mv $fafile ${fafile%.fa}.fna
+ echo "Renamed $(basename $fafile)"
+ done
+ touch "$LIBRARY_DIR/H_sapiens/lib.complete"
+ else
+ echo "Skipping download of human genome, already downloaded here."
+ fi
+ ;;
+ *)
+ echo "Unsupported library. Valid options are: "
+ echo " bacteria virus human"
+ ;;
+esac
diff --git a/scripts/download_taxonomy.sh b/scripts/download_taxonomy.sh
new file mode 100755
index 0000000..2b35a86
--- /dev/null
+++ b/scripts/download_taxonomy.sh
@@ -0,0 +1,60 @@
+#!/bin/bash
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+# Download NCBI taxonomy information for Kraken.
+# Designed to be called by kraken_build
+
+set -u # Protect against uninitialized vars.
+set -e # Stop on error
+
+TAXONOMY_DIR="$KRAKEN_DB_NAME/taxonomy"
+NCBI_SERVER="ftp.ncbi.nih.gov"
+FTP_SERVER="ftp://$NCBI_SERVER"
+THIS_DIR=$PWD
+
+mkdir -p "$TAXONOMY_DIR"
+cd "$TAXONOMY_DIR"
+
+if [ ! -e "gimap.dlflag" ]
+then
+ wget $FTP_SERVER/pub/taxonomy/gi_taxid_nucl.dmp.gz
+ touch gimap.dlflag
+ echo "Downloaded GI to taxon map"
+fi
+
+if [ ! -e "taxdump.dlflag" ]
+then
+ wget $FTP_SERVER/pub/taxonomy/taxdump.tar.gz
+ touch taxdump.dlflag
+ echo "Downloaded taxonomy tree data"
+fi
+
+if [ ! -e "gimap.flag" ]
+then
+ gunzip gi_taxid_nucl.dmp.gz
+ touch gimap.flag
+ echo "Uncompressed GI to taxon map"
+fi
+
+if [ ! -e "taxdump.flag" ]
+then
+ tar zxf taxdump.tar.gz
+ touch taxdump.flag
+ echo "Uncompressed taxonomy tree data"
+fi
diff --git a/scripts/kraken-build.broken b/scripts/kraken-build.broken
new file mode 100755
index 0000000..37804cf
--- /dev/null
+++ b/scripts/kraken-build.broken
@@ -0,0 +1,286 @@
+#!/usr/bin/perl
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+use strict;
+use warnings;
+use File::Basename;
+use Getopt::Long;
+
+my $PROG = basename $0;
+my $KRAKEN_DIR = "#####=KRAKEN_DIR=#####";
+
+# Test to see if the executables got moved, try to recover if we can
+if (! -e "$KRAKEN_DIR/classify") {
+ use Cwd 'abs_path';
+ $KRAKEN_DIR = dirname abs_path($0);
+}
+
+$ENV{"KRAKEN_DIR"} = $KRAKEN_DIR;
+$ENV{"PATH"} = "$KRAKEN_DIR:$ENV{PATH}";
+
+my $DEF_MINIMIZER_LEN = 15;
+my $DEF_KMER_LEN = 31;
+my $DEF_THREAD_CT = 1;
+
+my @VALID_LIBRARY_TYPES = qw/bacteria viruses human/;
+
+# Option/task option variables
+my (
+ $db,
+ $threads,
+ $minimizer_len,
+ $kmer_len,
+ $new_db,
+ $hash_size,
+ $max_db_size,
+ $work_on_disk,
+
+ $dl_taxonomy,
+ $dl_library,
+ $add_to_library,
+ $build,
+ $shrink,
+ $standard,
+ $upgrade,
+ $clean,
+);
+
+$threads = $DEF_THREAD_CT;
+$minimizer_len = $DEF_MINIMIZER_LEN;
+$kmer_len = $DEF_KMER_LEN;
+$work_on_disk = "";
+$hash_size = "";
+$max_db_size = "";
+
+# variables corresponding to task options
+my @TASK_LIST = (
+ \$dl_taxonomy,
+ \$dl_library,
+ \$add_to_library,
+ \$build,
+ \$shrink,
+ \$standard,
+ \$upgrade,
+ \$clean,
+);
+
+GetOptions(
+ "help" => \&display_help,
+ "version" => \&display_version,
+
+ "db=s" => \$db,
+ "threads=i" => \$threads,
+ "minimizer-len=i", \$minimizer_len,
+ "kmer-len=i", \$kmer_len,
+ "new-db=s", \$new_db,
+ "jellyfish-hash-size=s", \$hash_size,
+ "max-db-size=s", \$max_db_size,
+ "work-on-disk", \$work_on_disk,
+
+ "download-taxonomy" => \$dl_taxonomy,
+ "download-library=s" => \$dl_library,
+ "add-to-library=s" => \$add_to_library,
+ "build" => \$build,
+ "shrink=i" => \$shrink,
+ "upgrade" => \$upgrade,
+ "standard" => \$standard,
+ "clean" => \$clean,
+) or usage();
+
+if (@ARGV) {
+ warn "Extra arguments on command line.\n";
+ usage();
+}
+my $task_options = 0;
+for my $flag_ref (@TASK_LIST) {
+ defined($$flag_ref) and $task_options++;
+}
+if ($task_options > 1) {
+ warn "More than one task option selected.\n";
+ usage();
+}
+if ($task_options == 0) {
+ warn "Must select a task option.\n";
+ usage();
+}
+
+if (! defined $db) {
+ die "Must specify a database name\n";
+}
+if ($threads <= 0) {
+ die "Can't use nonpositive thread count of $threads\n";
+}
+if ($minimizer_len >= $kmer_len) {
+ die "Minimizer length ($minimizer_len) must be less than k ($kmer_len)\n";
+}
+if ($minimizer_len <= 0) {
+ die "Can't use nonpositive minimizer length of $minimizer_len\n";
+}
+if ($kmer_len <= 2) {
+ die "Can't use k of $kmer_len (must be >= 2)\n";
+}
+if ($kmer_len > 31) {
+ die "Can't use k of $kmer_len (must be <= 31)\n";
+}
+if ($hash_size !~ /^(\d+[kKmMgG]?)?$/) {
+ die "Illegal hash size string\n";
+}
+if ($max_db_size !~ /^$/ && $max_db_size <= 0) {
+ die "Can't have negative max database size.\n";
+}
+
+$ENV{"KRAKEN_DB_NAME"} = $db;
+$ENV{"KRAKEN_THREAD_CT"} = $threads;
+$ENV{"KRAKEN_MINIMIZER_LEN"} = $minimizer_len;
+$ENV{"KRAKEN_KMER_LEN"} = $kmer_len;
+$ENV{"KRAKEN_HASH_SIZE"} = $hash_size;
+$ENV{"KRAKEN_MAX_DB_SIZE"} = $max_db_size;
+$ENV{"KRAKEN_WORK_ON_DISK"} = $work_on_disk;
+
+if ($dl_taxonomy) {
+ download_taxonomy();
+}
+elsif (defined($dl_library)) {
+ download_library($dl_library);
+}
+elsif (defined($add_to_library)) {
+ add_to_library($add_to_library);
+}
+elsif (defined($shrink)) {
+ shrink_db($shrink);
+}
+elsif ($standard) {
+ standard_installation();
+}
+elsif ($build) {
+ build_database();
+}
+elsif ($clean) {
+ clean_database();
+}
+elsif ($upgrade) {
+ upgrade_database();
+}
+else {
+ usage();
+}
+
+exit -1;
+# END OF MAIN CODE.
+
+sub usage {
+ my $exit_code = @_ ? shift : 64;
+ print STDERR < 0)\n";
+ }
+ if ($percentage >= 100) {
+ die "Can't use shrink percentage of $percentage (must be < 100)\n";
+ }
+ if (! defined($new_db)) {
+ die "Must specify new database name to perform shrink task\n";
+ }
+ exec "shrink_db.sh", $percentage, $new_db;
+}
+
+sub standard_installation {
+ exec "standard_installation.sh";
+}
+
+sub build_database {
+ exec "build_kraken_db.sh";
+}
+
+sub clean_database {
+ exec "clean_db.sh";
+}
+
+sub upgrade_database {
+ exec "upgrade_db.sh";
+}
diff --git a/scripts/kraken-report.broken b/scripts/kraken-report.broken
new file mode 100755
index 0000000..eb60d15
--- /dev/null
+++ b/scripts/kraken-report.broken
@@ -0,0 +1,133 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+use File::Basename;
+use Getopt::Long;
+
+my $PROG = basename $0;
+my $show_zeros = 0;
+my $db_prefix = "";
+
+GetOptions(
+ "help" => \&display_help,
+ "version" => \&display_version,
+ "show-zeros" => \$show_zeros,
+ "db=s" => \$db_prefix,
+);
+
+sub display_help {
+ print STDERR "Usage: $PROG --db KRAKEN_DB_NAME [--show-zeros] \n";
+ exit 0;
+}
+
+sub display_version {
+ print "Kraken version #####=VERSION=#####\n";
+ print "Copyright 2013, Derrick Wood (dwood\@cs.umd.edu)\n";
+ exit 0;
+}
+
+my (%child_lists, %name_map, %rank_map);
+load_taxonomy($db_prefix);
+
+my %taxo_counts;
+my $seq_count = 0;
+$taxo_counts{0} = 0;
+while (<>) {
+ my @fields = split;
+ $taxo_counts{$fields[2]}++;
+ $seq_count++;
+}
+my $classified_count = $seq_count - $taxo_counts{0};
+
+my %clade_counts = %taxo_counts;
+dfs_summation(1);
+
+for (keys %name_map) {
+ $clade_counts{$_} ||= 0;
+}
+
+printf "%6.2f\t%d\t%d\t%s\t%d\t%s%s\n",
+ $clade_counts{0} * 100 / $seq_count,
+ $clade_counts{0}, $taxo_counts{0}, "U",
+ 0, "", "unclassified";
+dfs_report(1, 0);
+
+sub dfs_report {
+ my $node = shift;
+ my $depth = shift;
+ if (! $clade_counts{$node} && ! $show_zeros) {
+ return;
+ }
+ printf "%6.2f\t%d\t%d\t%s\t%d\t%s%s\n",
+ ($clade_counts{$node} || 0) * 100 / $seq_count,
+ ($clade_counts{$node} || 0),
+ ($taxo_counts{$node} || 0),
+ rank_code($rank_map{$node}),
+ $node,
+ " " x $depth,
+ $name_map{$node};
+ my $children = $child_lists{$node};
+ if ($children) {
+ my @sorted_children = sort { $clade_counts{$b} <=> $clade_counts{$a} } @$children;
+ for my $child (@sorted_children) {
+ dfs_report($child, $depth + 1);
+ }
+ }
+}
+
+sub rank_code {
+ my $rank = shift;
+ for ($rank) {
+ $_ eq "species" and return "S";
+ $_ eq "genus" and return "G";
+ $_ eq "family" and return "F";
+ $_ eq "order" and return "O";
+ $_ eq "class" and return "C";
+ $_ eq "phylum" and return "P";
+ }
+ return "-";
+}
+
+sub dfs_summation {
+ my $node = shift;
+ my $children = $child_lists{$node};
+ if ($children) {
+ for my $child (@$children) {
+ dfs_summation($child);
+ $clade_counts{$node} += ($clade_counts{$child} || 0);
+ }
+ }
+}
+
+sub load_taxonomy {
+ my $prefix = shift;
+
+ open NAMES, "<", "$prefix/taxonomy/names.dmp"
+ or die "$PROG: can't open names file: $!\n";
+ while () {
+ chomp;
+ s/\t\|$//;
+ my @fields = split /\t\|\t/;
+ my ($node_id, $name, $type) = @fields[0,1,3];
+ if ($type eq "scientific name") {
+ $name_map{$node_id} = $name;
+ }
+ }
+ close NAMES;
+
+ open NODES, "<", "$prefix/taxonomy/nodes.dmp"
+ or die "$PROG: can't open nodes file: $!\n";
+ while () {
+ chomp;
+ my @fields = split /\t\|\t/;
+ my ($node_id, $parent_id, $rank) = @fields[0,1,2];
+ if ($node_id == 1) {
+ $parent_id = 0;
+ }
+ $child_lists{$parent_id} ||= [];
+ push @{ $child_lists{$parent_id} }, $node_id;
+ $rank_map{$node_id} = $rank;
+ }
+ close NODES;
+}
diff --git a/scripts/kraken.broken b/scripts/kraken.broken
new file mode 100755
index 0000000..39027b0
--- /dev/null
+++ b/scripts/kraken.broken
@@ -0,0 +1,131 @@
+#!/usr/bin/perl
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+use strict;
+use warnings;
+use File::Basename;
+use Getopt::Long;
+
+my $PROG = basename $0;
+my $KRAKEN_DIR = "#####=KRAKEN_DIR=#####";
+
+# Test to see if the executables got moved, try to recover if we can
+if (! -e "$KRAKEN_DIR/classify") {
+ use Cwd 'abs_path';
+ $KRAKEN_DIR = dirname abs_path($0);
+}
+
+my $CLASSIFY = "$KRAKEN_DIR/classify";
+
+my $quick = 0;
+my $min_hits = 1;
+my $fastq_input = 0;
+my $db_prefix = "";
+my $threads = 1;
+my $preload = 0;
+my $unclassified_out;
+my $classified_out;
+my $outfile;
+
+GetOptions(
+ "help" => \&display_help,
+ "version" => \&display_version,
+ "db=s" => \$db_prefix,
+ "threads=i" => \$threads,
+ "fastq-input" => \$fastq_input,
+ "quick" => \$quick,
+ "min-hits=i" => \$min_hits,
+ "unclassified-out=s" => \$unclassified_out,
+ "classified-out=s" => \$classified_out,
+ "output=s" => \$outfile,
+ "preload" => \$preload
+);
+
+if (! @ARGV) {
+ print STDERR "Need to specify input filenames!\n";
+ usage();
+}
+
+my $taxonomy = "$db_prefix/taxonomy/nodes.dmp";
+if ($quick) {
+ undef $taxonomy; # Skip loading nodes file, not needed in quick mode
+}
+
+my $kdb_file = "$db_prefix/database.kdb";
+my $idx_file = "$db_prefix/database.idx";
+if (! -e $kdb_file) {
+ die "$PROG: $kdb_file does not exist!\n";
+}
+if (! -e $idx_file) {
+ die "$PROG: $idx_file does not exist!\n";
+}
+
+if ($min_hits > 1 && ! $quick) {
+ die "$PROG: --min_hits requires --quick to be specified\n";
+}
+
+my @flags;
+push @flags, "-d", $kdb_file;
+push @flags, "-i", $idx_file;
+push @flags, "-t", $threads if $threads > 1;
+push @flags, "-n", $taxonomy if defined $taxonomy;
+push @flags, "-q" if $quick;
+push @flags, "-m", $min_hits if $min_hits > 1;
+push @flags, "-f" if $fastq_input;
+push @flags, "-U", $unclassified_out if defined $unclassified_out;
+push @flags, "-C", $classified_out if defined $classified_out;
+push @flags, "-o", $outfile if defined $outfile;
+push @flags, "-M" if $preload;
+
+exec $CLASSIFY, @flags, @ARGV;
+
+sub usage {
+ my $exit_code = @_ ? shift : 64;
+ print STDERR <
+
+Options:
+ --db NAME Name for Kraken DB
+ --threads NUM Number of threads
+ --fastq-input Input is FASTQ, not FASTA format
+ --quick Quick operation (use first hit or hits)
+ --min-hits NUM In quick op., number of hits req'd for classification
+ NOTE: this is ignored if --quick is not specified
+ --unclassified-out FILENAME
+ Print unclassified sequences to filename
+ --classified-out FILENAME
+ Print classified sequences to filename
+ --output FILENAME Print output to filename (def. is stdout); "-" will
+ suppress normal output
+ --preload Loads DB into memory before classification
+ --help Print this message
+ --version Print version information
+EOF
+ exit $exit_code;
+}
+
+sub display_help {
+ usage(0);
+}
+
+sub display_version {
+ print "Kraken version #####=VERSION=#####\n";
+ print "Copyright 2013, Derrick Wood (dwood\@cs.umd.edu)\n";
+ exit 0;
+}
diff --git a/scripts/shrink_db.sh b/scripts/shrink_db.sh
new file mode 100755
index 0000000..b247eed
--- /dev/null
+++ b/scripts/shrink_db.sh
@@ -0,0 +1,51 @@
+#!/bin/bash
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+# Shrink a Kraken database
+# Designed to be called by kraken_build
+
+set -u # Protect against uninitialized vars.
+set -e # Stop on error
+set -o pipefail # Stop on failures in non-final pipeline commands
+
+percentage="$1"
+new_db="$2"
+
+OLD_DB_DIR="$KRAKEN_DB_NAME"
+NEW_DB_DIR="$new_db"
+
+if [ -e "$NEW_DB_DIR" ]
+then
+ echo "$new_db already exists ($NEW_DB_DIR), aborting shrink operation."
+ exit 1
+else
+ mkdir -p "$NEW_DB_DIR/taxonomy"
+fi
+
+cp "$OLD_DB_DIR/taxonomy/nodes.dmp" "$NEW_DB_DIR/taxonomy"
+cp "$OLD_DB_DIR/taxonomy/names.dmp" "$NEW_DB_DIR/taxonomy"
+db_shrink -p $percentage -d "$OLD_DB_DIR/database.kdb" \
+ -o "$NEW_DB_DIR/database.jdb.tmp"
+mv "$NEW_DB_DIR/database.jdb.tmp" "$NEW_DB_DIR/database.jdb"
+echo "Reduced database created, now sorting..."
+db_sort -M -t $KRAKEN_THREAD_CT -n $KRAKEN_MINIMIZER_LEN \
+ -d "$NEW_DB_DIR/database.jdb" -o "$NEW_DB_DIR/database.kdb.tmp" \
+ -i "$NEW_DB_DIR/database.idx"
+mv "$NEW_DB_DIR/database.kdb.tmp" "$NEW_DB_DIR/database.kdb"
+echo "Sort complete, database is ready."
diff --git a/scripts/standard_installation.sh b/scripts/standard_installation.sh
new file mode 100755
index 0000000..b97fb9e
--- /dev/null
+++ b/scripts/standard_installation.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+# Build the standard Kraken database
+# Designed to be called by kraken_build
+
+set -u # Protect against uninitialized vars.
+set -e # Stop on error
+set -o pipefail # Stop on failures in non-final pipeline commands
+
+WOD_FLAG=""
+if [ -n "$KRAKEN_WORK_ON_DISK" ]
+then
+ WOD_FLAG="--work-on-disk"
+fi
+
+kraken-build --db $KRAKEN_DB_NAME --download-taxonomy
+kraken-build --db $KRAKEN_DB_NAME --download-library bacteria
+kraken-build --db $KRAKEN_DB_NAME --download-library viruses
+kraken-build --db $KRAKEN_DB_NAME --build --threads $KRAKEN_THREAD_CT \
+ --jellyfish-hash-size "$KRAKEN_HASH_SIZE" \
+ --max-db-size "$KRAKEN_MAX_DB_SIZE" \
+ --minimizer-len $KRAKEN_MINIMIZER_LEN \
+ --kmer-len $KRAKEN_KMER_LEN \
+ $WOD_FLAG
diff --git a/scripts/upgrade_db.sh b/scripts/upgrade_db.sh
new file mode 100755
index 0000000..211e4f3
--- /dev/null
+++ b/scripts/upgrade_db.sh
@@ -0,0 +1,85 @@
+#!/bin/bash
+
+# Copyright 2013, Derrick Wood
+#
+# This file is part of the Kraken taxonomic sequence classification system.
+#
+# Kraken is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Kraken is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Kraken. If not, see .
+
+# Upgrade a pre-v0.10.0-beta Kraken DB to use scrambled minimizer order
+# Designed to be called by kraken_build
+
+set -u # Protect against uninitialized vars.
+set -e # Stop on error
+set -o pipefail # Stop on failures in non-final pipeline commands
+
+function report_time_elapsed() {
+ curr_time=$(date "+%s.%N")
+ perl -e '$time = $ARGV[1] - $ARGV[0];' \
+ -e '$sec = int($time); $nsec = $time - $sec;' \
+ -e '$min = int($sec/60); $sec %= 60;' \
+ -e '$hr = int($min/60); $min %= 60;' \
+ -e 'print "${hr}h" if $hr;' \
+ -e 'print "${min}m" if $min || $hr;' \
+ -e 'printf "%.3fs", $sec + $nsec;' \
+ $1 $curr_time
+}
+
+start_time=$(date "+%s.%N")
+
+DATABASE_DIR="$KRAKEN_DB_NAME"
+
+if [ ! -d "$DATABASE_DIR" ]
+then
+ echo "Can't find Kraken DB directory \"$KRAKEN_DB_NAME\""
+ exit 1
+fi
+cd "$DATABASE_DIR"
+
+MEMFLAG=""
+if [ -n "$KRAKEN_WORK_ON_DISK" ]
+then
+ MEMFLAG="-M"
+fi
+
+if [ -e "old_database.kdb" ]
+then
+ echo "old_database.kdb found - it appears database is already upgraded."
+ exit 1
+fi
+
+if [ ! -e "database.kdb" ]
+then
+ echo "Can't find database.kdb file!"
+ exit 1
+fi
+if [ ! -e "database.idx" ]
+then
+ echo "Can't find database.idx file!"
+ exit 1
+fi
+
+idx_size=$(stat -c '%s' database.idx)
+# Calculate minimizer length based on existing index size
+minimizer_len=$(perl -le 'print int(log(shift() / 8 - 2) / log(4))' $idx_size)
+
+db_sort $MEMFLAG -t $KRAKEN_THREAD_CT -n $minimizer_len -d database.kdb \
+ -o newdb.kdb -i newdb.idx
+mv database.idx old_database.idx
+mv database.kdb old_database.kdb
+mv newdb.idx database.idx
+mv newdb.kdb database.kdb
+
+echo "Database upgrade complete. [$(report_time_elapsed $start_time)]"
+echo "Old database files are at $KRAKEN_DB_NAME/old_database.{kdb,idx}"
diff --git a/src/Makefile b/src/Makefile
new file mode 100644
index 0000000..3ae5f94
--- /dev/null
+++ b/src/Makefile
@@ -0,0 +1,35 @@
+CXX = g++
+CXXFLAGS = -Wall -fopenmp -O3
+PROGS = db_sort set_lcas classify make_file_to_taxon_map db_shrink
+
+.PHONY: all install clean
+
+all: $(PROGS)
+
+install: $(PROGS)
+ cp $(PROGS) $(KRAKEN_DIR)/
+
+clean:
+ rm -f $(PROGS) *.o
+
+db_shrink: krakendb.o quickfile.o
+
+db_sort: krakendb.o quickfile.o
+
+set_lcas: krakendb.o quickfile.o krakenutil.o seqreader.o
+
+classify: krakendb.o quickfile.o krakenutil.o seqreader.o
+
+make_file_to_taxon_map: quickfile.o
+
+krakenutil.o: krakenutil.cpp krakenutil.hpp
+ $(CXX) $(CXXFLAGS) -c krakenutil.cpp
+
+krakendb.o: krakendb.cpp krakendb.hpp quickfile.hpp
+ $(CXX) $(CXXFLAGS) -c krakendb.cpp
+
+seqreader.o: seqreader.cpp seqreader.hpp quickfile.hpp
+ $(CXX) $(CXXFLAGS) -c seqreader.cpp
+
+quickfile.o: quickfile.cpp quickfile.hpp
+ $(CXX) $(CXXFLAGS) -c quickfile.cpp
diff --git a/src/classify.cpp b/src/classify.cpp
new file mode 100644
index 0000000..f312c58
--- /dev/null
+++ b/src/classify.cpp
@@ -0,0 +1,446 @@
+/*
+ * Copyright 2013, Derrick Wood
+ *
+ * This file is part of the Kraken taxonomic sequence classification system.
+ *
+ * Kraken is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Kraken is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Kraken. If not, see .
+ */
+
+#include "kraken_headers.hpp"
+#include "krakendb.hpp"
+#include "krakenutil.hpp"
+#include "quickfile.hpp"
+#include "seqreader.hpp"
+
+const size_t DEF_WORK_UNIT_SIZE = 500000;
+
+using namespace std;
+using namespace kraken;
+
+void parse_command_line(int argc, char **argv);
+void usage(int exit_code=EX_USAGE);
+void process_file(char *filename);
+void classify_sequence(DNASequence &dna, ostringstream &koss,
+ ostringstream &coss, ostringstream &uoss);
+string hitlist_string(vector &taxa, vector &ambig);
+set get_ancestry(uint32_t taxon);
+void report_stats(struct timeval time1, struct timeval time2);
+
+int Num_threads = 1;
+string DB_filename, Index_filename, Nodes_filename;
+bool Quick_mode = false;
+bool Fastq_input = false;
+bool Print_classified = false;
+bool Print_unclassified = false;
+bool Print_kraken = true;
+bool Populate_memory = false;
+uint32_t Minimum_hit_count = 1;
+map Parent_map;
+KrakenDB Database;
+string Classified_output_file, Unclassified_output_file, Kraken_output_file;
+ostream *Classified_output;
+ostream *Unclassified_output;
+ostream *Kraken_output;
+size_t Work_unit_size = DEF_WORK_UNIT_SIZE;
+
+uint64_t total_classified = 0;
+uint64_t total_sequences = 0;
+uint64_t total_bases = 0;
+
+int main(int argc, char **argv) {
+ #ifdef _OPENMP
+ omp_set_num_threads(1);
+ #endif
+
+ parse_command_line(argc, argv);
+ if (! Nodes_filename.empty())
+ Parent_map = build_parent_map(Nodes_filename);
+
+ if (Populate_memory)
+ cerr << "Loading database... ";
+
+ QuickFile db_file;
+ db_file.open_file(DB_filename);
+ if (Populate_memory)
+ db_file.load_file();
+ Database = KrakenDB(db_file.ptr());
+ KmerScanner::set_k(Database.get_k());
+
+ QuickFile idx_file;
+ idx_file.open_file(Index_filename);
+ if (Populate_memory)
+ idx_file.load_file();
+ KrakenDBIndex db_index(idx_file.ptr());
+ Database.set_index(&db_index);
+
+ if (Populate_memory)
+ cerr << "complete." << endl;
+
+ if (Print_classified) {
+ if (Classified_output_file == "-")
+ Classified_output = &cout;
+ else
+ Classified_output = new ofstream(Classified_output_file.c_str());
+ }
+
+ if (Print_unclassified) {
+ if (Unclassified_output_file == "-")
+ Unclassified_output = &cout;
+ else
+ Unclassified_output = new ofstream(Unclassified_output_file.c_str());
+ }
+
+ if (! Kraken_output_file.empty()) {
+ if (Kraken_output_file == "-")
+ Print_kraken = false;
+ else
+ Kraken_output = new ofstream(Kraken_output_file.c_str());
+ }
+ else
+ Kraken_output = &cout;
+
+ struct timeval tv1, tv2;
+ gettimeofday(&tv1, NULL);
+ for (int i = optind; i < argc; i++)
+ process_file(argv[i]);
+ gettimeofday(&tv2, NULL);
+
+ report_stats(tv1, tv2);
+
+ return 0;
+}
+
+void report_stats(struct timeval time1, struct timeval time2) {
+ time2.tv_usec -= time1.tv_usec;
+ time2.tv_sec -= time1.tv_sec;
+ if (time2.tv_usec < 0) {
+ time2.tv_sec--;
+ time2.tv_usec += 1000000;
+ }
+ double seconds = time2.tv_usec;
+ seconds /= 1e6;
+ seconds += time2.tv_sec;
+
+ cerr << "\r";
+ fprintf(stderr,
+ "%llu sequences (%.2f Mbp) processed in %.3fs (%.1f Kseq/m, %.2f Mbp/m).\n",
+ (unsigned long long) total_sequences, total_bases / 1.0e6, seconds,
+ total_sequences / 1.0e3 / (seconds / 60),
+ total_bases / 1.0e6 / (seconds / 60) );
+ fprintf(stderr, " %llu sequences classified (%.2f%%)\n",
+ (unsigned long long) total_classified, total_classified * 100.0 / total_sequences);
+ fprintf(stderr, " %llu sequences unclassified (%.2f%%)\n",
+ (unsigned long long) (total_sequences - total_classified),
+ (total_sequences - total_classified) * 100.0 / total_sequences);
+}
+
+void process_file(char *filename) {
+ string file_str(filename);
+ DNASequenceReader *reader;
+ DNASequence dna;
+
+ if (Fastq_input)
+ reader = new FastqReader(file_str);
+ else
+ reader = new FastaReader(file_str);
+
+ vector work_units[Num_threads];
+ ostringstream kraken_output[Num_threads],
+ classified_output[Num_threads],
+ unclassified_output[Num_threads];
+ while (reader->is_valid()) {
+ // Get work for each thread
+ for (int i = 0; i < Num_threads; i++) {
+ work_units[i].clear();
+ size_t total_nt = 0;
+ while (total_nt < Work_unit_size) {
+ dna = reader->next_sequence();
+ if (! reader->is_valid())
+ break;
+ total_sequences++;
+ work_units[i].push_back(dna);
+ total_nt += dna.seq.size();
+ }
+ total_bases += total_nt;
+ }
+
+ // Classification loop
+ #pragma omp parallel for
+ for (int i = 0; i < Num_threads; i++) {
+ if (Print_kraken)
+ kraken_output[i].str("");
+ if (Print_classified)
+ classified_output[i].str("");
+ if (Print_unclassified)
+ unclassified_output[i].str("");
+ for (size_t j = 0; j < work_units[i].size(); j++)
+ classify_sequence( work_units[i][j], kraken_output[i],
+ classified_output[i], unclassified_output[i] );
+ }
+
+ // Report loop
+ for (int i = 0; i < Num_threads; i++) {
+ if (Print_kraken)
+ (*Kraken_output) << kraken_output[i].str();
+ if (Print_classified)
+ (*Classified_output) << classified_output[i].str();
+ if (Print_unclassified)
+ (*Unclassified_output) << unclassified_output[i].str();
+ }
+
+ cerr << "\rProcessed " << total_sequences << " sequences (" << total_bases << " bp) ...";
+ }
+
+ delete reader;
+}
+
+void classify_sequence(DNASequence &dna, ostringstream &koss,
+ ostringstream &coss, ostringstream &uoss) {
+ vector taxa;
+ vector ambig_list;
+ map hit_counts;
+ uint64_t *kmer_ptr;
+ uint32_t taxon = 0;
+ uint32_t hits = 0; // only maintained if in quick mode
+
+ uint64_t current_bin_key;
+ int64_t current_min_pos = 1;
+ int64_t current_max_pos = 0;
+
+ if (dna.seq.size() >= Database.get_k()) {
+ KmerScanner scanner(dna.seq);
+ while ((kmer_ptr = scanner.next_kmer()) != NULL) {
+ taxon = 0;
+ if (scanner.ambig_kmer()) {
+ ambig_list.push_back(1);
+ }
+ else {
+ ambig_list.push_back(0);
+ uint32_t *val_ptr = Database.kmer_query(
+ Database.canonical_representation(*kmer_ptr),
+ ¤t_bin_key,
+ ¤t_min_pos, ¤t_max_pos
+ );
+ taxon = val_ptr ? *val_ptr : 0;
+ if (taxon) {
+ hit_counts[taxon]++;
+ if (Quick_mode && ++hits >= Minimum_hit_count)
+ break;
+ }
+ }
+ taxa.push_back(taxon);
+ }
+ }
+
+ uint32_t call = 0;
+ if (Quick_mode)
+ call = hits >= Minimum_hit_count ? taxon : 0;
+ else
+ call = resolve_tree(hit_counts, Parent_map);
+
+ if (call)
+ #pragma omp atomic
+ total_classified++;
+
+ if (Print_unclassified || Print_classified) {
+ ostringstream *oss_ptr = call ? &coss : &uoss;
+ bool print = call ? Print_classified : Print_unclassified;
+ if (print) {
+ if (Fastq_input) {
+ (*oss_ptr) << "@" << dna.id << endl
+ << dna.seq << endl
+ << "+" << endl
+ << dna.quals << endl;
+ }
+ else {
+ (*oss_ptr) << ">" << dna.id << endl
+ << dna.seq << endl;
+ }
+ }
+ }
+
+ if (! Print_kraken)
+ return;
+
+ if (call) {
+ koss << "C\t";
+ }
+ else {
+ koss << "U\t";
+ }
+ koss << dna.id << "\t" << call << "\t" << dna.seq.size() << "\t";
+
+ if (Quick_mode) {
+ koss << "Q:" << hits;
+ }
+ else {
+ if (taxa.empty())
+ koss << "0:0";
+ else
+ koss << hitlist_string(taxa, ambig_list);
+ }
+
+ koss << endl;
+}
+
+string hitlist_string(vector &taxa, vector &ambig)
+{
+ int64_t last_code;
+ int code_count = 1;
+ ostringstream hitlist;
+
+ if (ambig[0]) { last_code = -1; }
+ else { last_code = taxa[0]; }
+
+ for (size_t i = 1; i < taxa.size(); i++) {
+ int64_t code;
+ if (ambig[i]) { code = -1; }
+ else { code = taxa[i]; }
+
+ if (code == last_code) {
+ code_count++;
+ }
+ else {
+ if (last_code >= 0) {
+ hitlist << last_code << ":" << code_count << " ";
+ }
+ else {
+ hitlist << "A:" << code_count << " ";
+ }
+ code_count = 1;
+ last_code = code;
+ }
+ }
+ if (last_code >= 0) {
+ hitlist << last_code << ":" << code_count;
+ }
+ else {
+ hitlist << "A:" << code_count;
+ }
+ return hitlist.str();
+}
+
+set get_ancestry(uint32_t taxon) {
+ set path;
+
+ while (taxon > 0) {
+ path.insert(taxon);
+ taxon = Parent_map[taxon];
+ }
+ return path;
+}
+
+void parse_command_line(int argc, char **argv) {
+ int opt;
+ int sig;
+
+ if (argc > 1 && strcmp(argv[1], "-h") == 0)
+ usage(0);
+ while ((opt = getopt(argc, argv, "d:i:t:u:n:m:o:qfC:U:M")) != -1) {
+ switch (opt) {
+ case 'd' :
+ DB_filename = optarg;
+ break;
+ case 'i' :
+ Index_filename = optarg;
+ break;
+ case 't' :
+ sig = atoi(optarg);
+ if (sig <= 0)
+ errx(EX_USAGE, "can't use nonpositive thread count");
+ #ifdef _OPENMP
+ Num_threads = sig;
+ omp_set_num_threads(Num_threads);
+ #endif
+ break;
+ case 'n' :
+ Nodes_filename = optarg;
+ break;
+ case 'q' :
+ Quick_mode = true;
+ break;
+ case 'm' :
+ sig = atoi(optarg);
+ if (sig <= 0)
+ errx(EX_USAGE, "can't use nonpositive minimum hit count");
+ Minimum_hit_count = sig;
+ break;
+ case 'f' :
+ Fastq_input = true;
+ break;
+ case 'C' :
+ Print_classified = true;
+ Classified_output_file = optarg;
+ break;
+ case 'U' :
+ Print_unclassified = true;
+ Unclassified_output_file = optarg;
+ break;
+ case 'o' :
+ Kraken_output_file = optarg;
+ break;
+ case 'u' :
+ sig = atoi(optarg);
+ if (sig <= 0)
+ errx(EX_USAGE, "can't use nonpositive work unit size");
+ Work_unit_size = sig;
+ break;
+ case 'M' :
+ Populate_memory = true;
+ break;
+ default:
+ usage();
+ break;
+ }
+ }
+
+ if (DB_filename.empty()) {
+ cerr << "Missing mandatory option -d" << endl;
+ usage();
+ }
+ if (Index_filename.empty()) {
+ cerr << "Missing mandatory option -i" << endl;
+ usage();
+ }
+ if (Nodes_filename.empty() && ! Quick_mode) {
+ cerr << "Must specify one of -q or -n" << endl;
+ usage();
+ }
+ if (optind == argc) {
+ cerr << "No sequence data files specified" << endl;
+ }
+}
+
+void usage(int exit_code) {
+ cerr << "Usage: classify [options] " << endl
+ << endl
+ << "Options: (*mandatory)" << endl
+ << "* -d filename Kraken DB filename" << endl
+ << "* -i filename Kraken DB index filename" << endl
+ << " -n filename NCBI Taxonomy nodes file" << endl
+ << " -o filename Output file for Kraken output" << endl
+ << " -t # Number of threads" << endl
+ << " -u # Thread work unit size (in bp)" << endl
+ << " -q Quick operation" << endl
+ << " -m # Minimum hit count (ignored w/o -q)" << endl
+ << " -C filename Print classified sequences" << endl
+ << " -U filename Print unclassified sequences" << endl
+ << " -f Input is in FASTQ format" << endl
+ << " -M Preload database files" << endl
+ << " -h Print this message" << endl
+ << endl
+ << "At least one FASTA or FASTQ file must be specified." << endl
+ << "Kraken output is to standard output by default." << endl;
+ exit(exit_code);
+}
diff --git a/src/db_shrink.cpp b/src/db_shrink.cpp
new file mode 100644
index 0000000..abb4f58
--- /dev/null
+++ b/src/db_shrink.cpp
@@ -0,0 +1,126 @@
+/*
+ * Copyright 2013, Derrick Wood
+ *
+ * This file is part of the Kraken taxonomic sequence classification system.
+ *
+ * Kraken is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Kraken is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Kraken. If not, see .
+ */
+
+#include "kraken_headers.hpp"
+#include "quickfile.hpp"
+#include "krakendb.hpp"
+
+using namespace std;
+using namespace kraken;
+
+string Input_DB_filename, Output_DB_filename;
+int Shrink_percentage = 0;
+bool Operate_in_RAM = false;
+
+static void parse_command_line(int argc, char **argv);
+static void usage(int exit_code=EX_USAGE);
+
+int main(int argc, char **argv) {
+ #ifdef _OPENMP
+ omp_set_num_threads(1);
+ #endif
+
+ parse_command_line(argc, argv);
+
+ QuickFile input_db_file(Input_DB_filename);
+ KrakenDB input_db(input_db_file.ptr());
+
+ size_t new_file_size = input_db.header_size();
+ uint64_t key_ct = input_db.get_key_ct();
+ uint64_t new_key_ct = key_ct * Shrink_percentage / 100;
+ uint64_t pair_size = input_db.pair_size();
+ new_file_size += new_key_ct * pair_size;
+
+ QuickFile output_file;
+ char *temp_file = NULL;
+ char *outptr;
+ if (Operate_in_RAM) {
+ temp_file = new char[new_file_size];
+ }
+ else {
+ output_file.open_file(Output_DB_filename, "rw", new_file_size);
+ temp_file = output_file.ptr();
+ }
+ outptr = temp_file;
+ // Copy input header to output file
+ memcpy(outptr, input_db.get_ptr(), input_db.header_size());
+ // Change key count
+ memcpy(outptr + 48, &new_key_ct, 8);
+ outptr += input_db.header_size();
+
+ char *inptr = input_db.get_pair_ptr();
+ // For each 100 consecutive pairs, select the last P pairs of the block
+ for (uint64_t i = 0; i < new_key_ct; i += Shrink_percentage) {
+ inptr += (100 - Shrink_percentage) * pair_size;
+ outptr += Shrink_percentage * pair_size;
+ memcpy(outptr, inptr, Shrink_percentage * pair_size);
+ inptr += Shrink_percentage * pair_size;
+ }
+
+ input_db_file.close_file();
+
+ if (Operate_in_RAM) {
+ // Actual file hasn't been opened yet if -M used
+ output_file.open_file(Output_DB_filename, "w", new_file_size);
+ memcpy(output_file.ptr(), temp_file, new_file_size);
+ delete temp_file;
+ }
+
+ output_file.close_file();
+
+ return 0;
+}
+
+void parse_command_line(int argc, char **argv) {
+ int opt;
+ int sig;
+
+ if (argc > 1 && strcmp(argv[1], "-h") == 0)
+ usage(0);
+ while ((opt = getopt(argc, argv, "d:o:p:M")) != -1) {
+ switch (opt) {
+ case 'p' :
+ sig = atoi(optarg);
+ if (sig < 1 || sig >= 100)
+ errx(EX_USAGE, "shrink percentage out of range");
+ Shrink_percentage = sig;
+ break;
+ case 'd' :
+ Input_DB_filename = optarg;
+ break;
+ case 'o' :
+ Output_DB_filename = optarg;
+ break;
+ case 'M' :
+ Operate_in_RAM = true;
+ break;
+ default:
+ usage();
+ break;
+ }
+ }
+
+ if (Input_DB_filename.empty() || Output_DB_filename.empty() || ! Shrink_percentage)
+ usage();
+}
+
+void usage(int exit_code) {
+ cerr << "Usage: db_shrink [-M] <-d input db> <-o output db> <-p percentage>\n";
+ exit(exit_code);
+}
diff --git a/src/db_sort.cpp b/src/db_sort.cpp
new file mode 100644
index 0000000..1d87d5a
--- /dev/null
+++ b/src/db_sort.cpp
@@ -0,0 +1,187 @@
+/*
+ * Copyright 2013, Derrick Wood
+ *
+ * This file is part of the Kraken taxonomic sequence classification system.
+ *
+ * Kraken is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Kraken is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Kraken. If not, see .
+ */
+
+#include "kraken_headers.hpp"
+#include "quickfile.hpp"
+#include "krakendb.hpp"
+
+using namespace std;
+using namespace kraken;
+
+string Input_DB_filename, Output_DB_filename, Index_filename;
+uint8_t Bin_key_nt = 15;
+int Num_threads = 1;
+bool Zero_vals = false;
+bool Operate_in_RAM = false;
+#ifdef _OPENMP
+omp_lock_t *Locks;
+#endif
+
+static void parse_command_line(int argc, char **argv);
+static void bin_and_sort_data(KrakenDB &in, KrakenDB &out);
+static void usage(int exit_code=EX_USAGE);
+
+int main(int argc, char **argv) {
+ #ifdef _OPENMP
+ omp_set_num_threads(1);
+ #endif
+
+ parse_command_line(argc, argv);
+
+ QuickFile input_db_file(Input_DB_filename);
+ KrakenDB input_db(input_db_file.ptr());
+
+ input_db.make_index(Index_filename, Bin_key_nt);
+ QuickFile index_file(Index_filename);
+ KrakenDBIndex db_index(index_file.ptr());
+ input_db.set_index(&db_index);
+
+ // Copy header from input DB to output DB, reopen output DB in R/W
+ // open/reopen necessary due to "feature" of QuickFile/KrakenDB code
+ // (could be skipped if we didn't want to use KrakenDB features in basd()
+ QuickFile output_file;
+ char *temp_file;
+ if (Operate_in_RAM) {
+ temp_file = new char[ input_db_file.size() ];
+ }
+ else {
+ output_file.open_file(Output_DB_filename, "w", input_db_file.size());
+ temp_file = output_file.ptr();
+ }
+ memcpy(temp_file, input_db_file.ptr(), input_db.header_size());
+ if (! Operate_in_RAM) {
+ output_file.close_file();
+ output_file.open_file(Output_DB_filename, "rw");
+ temp_file = output_file.ptr();
+ }
+ KrakenDB output_db(temp_file);
+
+ bin_and_sort_data(input_db, output_db);
+
+ if (Operate_in_RAM) {
+ size_t filesize = input_db_file.size();
+ input_db_file.close_file();
+ output_file.open_file(Output_DB_filename, "w", filesize);
+ memcpy(output_file.ptr(), temp_file, filesize);
+ }
+ return 0;
+}
+
+static void bin_and_sort_data(KrakenDB &in, KrakenDB &out) {
+ char *in_ptr = in.get_pair_ptr();
+ char *out_ptr = out.get_pair_ptr();
+ uint8_t nt = in.get_index()->indexed_nt();
+ uint64_t *offsets = in.get_index()->get_array();
+ uint64_t entries = 1ull << (nt * 2);
+
+ #ifdef _OPENMP
+ Locks = new omp_lock_t[entries];
+ for (uint64_t i = 0; i < entries; i++)
+ omp_init_lock(&Locks[i]);
+ #endif
+
+ // Create a copy of the offsets array for use as insertion positions
+ vector pos(offsets, offsets + entries);
+ #pragma omp parallel for schedule(dynamic,400)
+ for (uint64_t i = 0; i < in.get_key_ct(); i++) {
+ uint64_t bin_key = in.bin_key(* (uint64_t *)(in_ptr + i * in.pair_size()));
+ #ifdef _OPENMP
+ omp_set_lock(&Locks[bin_key]);
+ #endif
+ #pragma omp flush(pos)
+ char *pair_pos = out_ptr + in.pair_size() * pos[bin_key];
+ // Copy pair into correct bin (but not final position)
+ memcpy(pair_pos, in_ptr + i * in.pair_size(), in.pair_size());
+ if (Zero_vals)
+ memset(pair_pos + in.get_key_len(), 0, in.get_val_len());
+ #pragma omp flush(pos)
+ pos[bin_key]++;
+ #ifdef _OPENMP
+ omp_unset_lock(&Locks[bin_key]);
+ #endif
+ }
+
+ #ifdef _OPENMP
+ for (uint64_t i = 0; i < entries; i++)
+ omp_destroy_lock(&Locks[i]);
+ delete Locks;
+ #endif
+
+ // Sort all bins
+ #pragma omp parallel for schedule(dynamic)
+ for (uint64_t i = 0; i < entries; i++) {
+ qsort(out_ptr + offsets[i] * out.pair_size(),
+ offsets[i+1] - offsets[i], out.pair_size(),
+ KrakenDB::pair_cmp);
+ }
+}
+
+void parse_command_line(int argc, char **argv) {
+ int opt;
+ int sig;
+
+ if (argc > 1 && strcmp(argv[1], "-h") == 0)
+ usage(0);
+ while ((opt = getopt(argc, argv, "n:d:o:i:t:zM")) != -1) {
+ switch (opt) {
+ case 'n' :
+ sig = atoi(optarg);
+ if (sig < 1 || sig > 31)
+ errx(EX_USAGE, "bin key length out of range");
+ Bin_key_nt = (uint8_t) sig;
+ break;
+ case 'd' :
+ Input_DB_filename = optarg;
+ break;
+ case 'o' :
+ Output_DB_filename = optarg;
+ break;
+ case 'i' :
+ Index_filename = optarg;
+ break;
+ case 'M' :
+ Operate_in_RAM = true;
+ break;
+ case 't' :
+ sig = atoi(optarg);
+ if (sig <= 0)
+ errx(EX_USAGE, "can't use nonpositive thread count");
+ #ifdef _OPENMP
+ Num_threads = sig;
+ omp_set_num_threads(Num_threads);
+ #endif
+ break;
+ case 'z' :
+ Zero_vals = true;
+ break;
+ default:
+ usage();
+ break;
+ }
+ }
+
+ if (Input_DB_filename.empty() || Output_DB_filename.empty()
+ || Index_filename.empty())
+ usage();
+}
+
+void usage(int exit_code) {
+ cerr << "Usage: db_sort [-z] [-M] [-t threads] [-n nt] <-d input db> <-o output db> <-i output idx>\n";
+ exit(exit_code);
+}
diff --git a/src/kraken_headers.hpp b/src/kraken_headers.hpp
new file mode 100644
index 0000000..0b691f7
--- /dev/null
+++ b/src/kraken_headers.hpp
@@ -0,0 +1,31 @@
+#ifndef KRAKEN_HEADERS_HPP
+#define KRAKEN_HEADERS_HPP
+
+#ifndef _XOPEN_SOURCE
+#define _XOPEN_SOURCE 1
+#endif
+
+#include
+#include
+#include
+#include
+#include
+#include
+#include
+#include
+#include