Merge pull request #257 from aidenlab/fix-encode-mega-stats

#!/usr/bin/awk -f

##########

#The MIT License (MIT)

#

# Copyright (c) 2015 Aiden Lab

#

# 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

# furnished to do so, subject to the following conditions:

#

# The above copyright notice and this permission notice shall be included in

# all copies or substantial portions of the Software.

#

#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

#  THE SOFTWARE.

##########

# Helper script for taking in multiple inter.txt and producing sums

# Juicer version 2.0

$1=="Sequenced"{

gsub(/,/,"",$4);

 total=total+$4;

}

$1=="Unmapped:"{

gsub(/,/,"",$2);

 unmapped=unmapped+$2

}

$1=="Normal"{

gsub(/,/,"",$3);

 regular=regular+$3}

$1=="Chimeric" && $2=="Paired:"{

gsub(/,/,"",$3);

 normal=normal+$3}

$2=="Ambiguous:"{

gsub(/,/,"",$3);

 abnorm=abnorm+$3}

$1=="Alignable"{

gsub(/,/,"",$4);

 alignable=alignable+$4}

$1=="Unique" {

gsub(/,/,"",$3);

 dedup=dedup+$3}

$1=="Duplicates:"{

gsub(/,/,"",$3);

 dups=dups+$3}

$1=="Ligation"{

gsub(/,/,"",$4);

 ligs=ligs+$4}

$1=="Single"{

gsub(/,/,"",$3);

 single=single+$3}

$1=="Average"{

 avg_insert=avg_insert+$4;

}

END{

 printf("%s %'d\n", "Sequenced Read Pairs:", total);

 printf(" %s %'d (%0.2f%)\n", "Normal Paired:", regular, regular*100/total);

 printf(" %s %'d (%0.2f%)\n", "Chimeric Paired:", normal, normal*100/total);

 printf(" %s %'d (%0.2f%)\n", "Chimeric Ambiguous:", abnorm, abnorm*100/total);

 printf(" %s %'d (%0.2f%)\n", "Unmapped:", unmapped, unmapped*100/total);

 printf(" %s %'d (%0.2f%)\n", "Ligation Motif Present:", ligs, ligs*100/total);

 printf(" %s %'d (%0.2f%)\n", "Single Alignment:", single, single*100/total);

 printf(" %s %0.2f\n", "Average insert size:", avg_insert/NR);

 printf(" %s %'d (%0.2f%)\n", "Alignable (Normal+Chimeric Paired):", alignable, alignable*100/total);

 printf("%s %'d\n", "Unique Reads:", dedup);

 printf("%s %'d\n", "Duplicates:", dups);

}

    merged_names30=$(find -L "${topDir}" | grep merged30.txt | tr '\n' ' ')

fi

inter_names=$(find -L "${topDir}" | grep inter.txt | tr '\n' ' ')

inter_30_names=$(find -L "${topDir}" | grep inter_30.txt | tr '\n' ' ')

inter_hist_names=$(find -L "${topDir}" | grep inter_hists.m | tr '\n' ' ')

inter_30_hist_names=$(find -L "${topDir}" | grep inter_30_hists.m | tr '\n' ' ')

## Create output directory, exit if already exists

if [[ -d "${outputDir}" ]] && [ -z $final ] && [ -z $postproc ]

if [ -z $final ] && [ -z $postproc ]

then

    # Create top statistics file from all inter.txt files found under current dir

    awk -f "${juiceDir}"/scripts/common/makemega_addstats.awk "${inter_names}" > "${outputDir}"/inter.txt

    java -Xmx2g -jar "${juiceDir}"/scripts/common/merge-stats.jar "$outputDir"/inter "${inter_names}"

    java -Xmx2g -jar "${juiceDir}"/scripts/common/merge-stats.jar "$outputDir"/inter_30 "${inter_30_names}"

    java -Xmx2g -jar "${juiceDir}"/scripts/common/merge-stats.jar "$outputDir"/inter "${inter_hist_names}"

    java -Xmx2g -jar "${juiceDir}"/scripts/common/merge-stats.jar "$outputDir"/inter_30 "${inter_30_hist_names}"

    echo "(-: Finished creating top stats files."

    cp "${outputDir}"/inter.txt "${outputDir}"/inter_30.txt

    sort --parallel=40 -T "${tmpdir}" -m -k2,2d -k6,6d "${merged_names}" > "${outputDir}"/merged1.txt

    sort --parallel=40 -T "${tmpdir}" -m -k2,2d -k6,6d "${merged_names30}" > "${outputDir}"/merged30.txt

    echo "(-: Finished sorting all files into a single merge."

    "${juiceDir}"/scripts/common/juicer_tools statistics "$site_file" "$outputDir"/inter.txt "$outputDir"/merged1.txt "$genomeID"

    "${juiceDir}"/scripts/common/juicer_tools statistics "$site_file" "$outputDir"/inter_30.txt "$outputDir"/merged30.txt "$genomeID"

    mkdir "${tempdirPre}"

	  if [[ $threadsHic -gt 1 ]] && [[ ! -s "${outputDir}"/merged1_index.txt ]]