From d21597aaa01ac546821568515975fb77b3aa6dc1 Mon Sep 17 00:00:00 2001
From: arangrhie <arrhie@gmail.com>
Date: Fri, 7 Feb 2020 10:25:48 -0500
Subject: [PATCH] clean up and move merqury

---
 README.md                               |  10 +-
 scripts/README.md                       | 232 ------------------------
 scripts/_submit_cn.sh                   |  33 ----
 scripts/_submit_cn_hap.sh               | 104 -----------
 scripts/_submit_meryl2_build.sh         | 161 ----------------
 scripts/_submit_meryl2_build_10x.sh     | 105 -----------
 scripts/_submit_meryl2_build_hapmers.sh | 135 --------------
 scripts/_submit_split.sh                |  33 ----
 scripts/build/concat_splits.sh          |  23 ---
 scripts/build/kmerHistToPloidyDepth.jar | Bin 20371 -> 0 bytes
 scripts/build/meryl2_count.sh           |  58 ------
 scripts/build/meryl2_count_10x.sh       |  55 ------
 scripts/build/meryl2_diff.sh            |  35 ----
 scripts/build/meryl2_filt.sh            |  30 ---
 scripts/build/meryl2_hapmers.sh         |  79 --------
 scripts/build/meryl2_union_sum.sh       | 119 ------------
 scripts/build/split.sh                  |  56 ------
 scripts/build/split_10x.sh              |  56 ------
 scripts/cn_hap.sh                       |  62 -------
 scripts/eval/bedCalcN50.jar             | Bin 35204 -> 0 bytes
 scripts/eval/spectra-cn.sh              | 225 -----------------------
 scripts/plot/plot_blob.R                |  47 -----
 scripts/plot/plot_block.sh              |  58 ------
 scripts/plot/plot_spectra_asm.R         |  53 ------
 scripts/plot/plot_spectra_cn.R          |  66 -------
 scripts/trio/bedMerToPhaseBlock.jar     | Bin 31354 -> 0 bytes
 scripts/trio/exclude_reads.sh           |  21 ---
 scripts/trio/fastaGetGaps.jar           | Bin 18792 -> 0 bytes
 scripts/trio/hap_blob.sh                |  74 --------
 scripts/trio/phase_block.sh             |  68 -------
 scripts/trio/spectra-hap.sh             | 107 -----------
 31 files changed, 2 insertions(+), 2103 deletions(-)
 delete mode 100644 scripts/README.md
 delete mode 100755 scripts/_submit_cn.sh
 delete mode 100755 scripts/_submit_cn_hap.sh
 delete mode 100755 scripts/_submit_meryl2_build.sh
 delete mode 100755 scripts/_submit_meryl2_build_10x.sh
 delete mode 100755 scripts/_submit_meryl2_build_hapmers.sh
 delete mode 100755 scripts/_submit_split.sh
 delete mode 100755 scripts/build/concat_splits.sh
 delete mode 100755 scripts/build/kmerHistToPloidyDepth.jar
 delete mode 100755 scripts/build/meryl2_count.sh
 delete mode 100755 scripts/build/meryl2_count_10x.sh
 delete mode 100755 scripts/build/meryl2_diff.sh
 delete mode 100755 scripts/build/meryl2_filt.sh
 delete mode 100755 scripts/build/meryl2_hapmers.sh
 delete mode 100755 scripts/build/meryl2_union_sum.sh
 delete mode 100755 scripts/build/split.sh
 delete mode 100755 scripts/build/split_10x.sh
 delete mode 100755 scripts/cn_hap.sh
 delete mode 100755 scripts/eval/bedCalcN50.jar
 delete mode 100755 scripts/eval/spectra-cn.sh
 delete mode 100755 scripts/plot/plot_blob.R
 delete mode 100755 scripts/plot/plot_block.sh
 delete mode 100755 scripts/plot/plot_spectra_asm.R
 delete mode 100755 scripts/plot/plot_spectra_cn.R
 delete mode 100755 scripts/trio/bedMerToPhaseBlock.jar
 delete mode 100755 scripts/trio/exclude_reads.sh
 delete mode 100755 scripts/trio/fastaGetGaps.jar
 delete mode 100755 scripts/trio/hap_blob.sh
 delete mode 100755 scripts/trio/phase_block.sh
 delete mode 100755 scripts/trio/spectra-hap.sh

diff --git a/README.md b/README.md
index 2499f90..32cab25 100644
--- a/README.md
+++ b/README.md
@@ -24,13 +24,7 @@ export PATH=/path/to/meryl/bin:$PATH
 This is 'sequence', a utility for working with sequence files.
 
 
-# Scripts
+# Evaluate assemblies with k-mers and more
 
-Here, bash scripts are provided to give a guideline for the following use-cases:
+See [Merqury](https://github.com/marbl/merqury).
 
-1.	[Build k-mer dbs in batches](https://github.com/marbl/meryl/tree/master/scripts#1-build-k-mer-dbs)
-2.	[Copy-number comparison (spectra-cn and spectra-hap)](https://github.com/marbl/meryl/tree/master/scripts#2-copy-number-comparison-spectra-cn)
-3.	[Haplotype specific mers for trio binning and making blob-plots](https://github.com/marbl/meryl/tree/master/scripts#3-haplotype-specific-mers-for-trio-binning-and-making-blob-plots)
-4.  [Include or exclude read pairs having specific kmers in one of the reads](https://github.com/marbl/meryl/blob/master/scripts/README.md#4-include-or-exclude-read-pairs-having-specific-kmers-in-one-of-the-reads)
-
-See [scripts](https://github.com/marbl/meryl/tree/master/scripts) for more details.
diff --git a/scripts/README.md b/scripts/README.md
deleted file mode 100644
index 0279114..0000000
--- a/scripts/README.md
+++ /dev/null
@@ -1,232 +0,0 @@
-# Scripts
-
-Here, bash scripts are provided to provide guidelines for the following purposes:
-
-1.	Build k-mer dbs in batches
-2.	Copy-number comparison (spectra-cn and spectra-hap)
-3.	Haplotype specific mers for trio binning and making blob-plots
-
-All scripts are tested on slurm environment for diploid genomes up to 3.3Gb.
-Modify the `_submit_*` scripts to match your system.
-`cpus` and `mem` are suggestive.
-
-
-# 1. Build k-mer dbs
-
-`_submit_meryl2_build.sh` is doing the following 1. Build and 2. Merge steps automatically.
-`_submit_meryl2_build_10x.sh` trims the 10X barcodes from illumina reads, and runs the 1. Build 2. Merge steps.
-The barcode trimming step uses `scaff_reads` from [scaff10x](https://github.com/wtsi-hpag/Scaff10X).
-
-## 1. Build
-
-Count k-mers in <in.sequence>, could be fastq/fasta file, gzipped or not.
-
-```
-meryl count k=$k_size output $output.meryl <in.sequence>
-```
-
-Will generate canonical k-mer counts.
-
-`Threads`: By default, meryl uses the maximum number of cores available, up to 64.
-This can be limited by defining `threads=$cores`.
-If you want to see results faster, split the <in.sequence> file to multiple pieces and count each kmers and merge at the end.
-
-`Memory`: Meryl automatically detects available memory and uses that.
-To prevent overhead for allocating too much memory, use something like `memory=48` which will use up to 48G.
-When the k-mer space is too big and requires more memory, meryl automatically splits countig jobs in batches and merges at the end.
-
-Run `meryl`  with no args to see more details.
-
-## 2. Merge
-
-If counted from multiple fastq files, merge them at the end.
-```
-ulimit -Sn 32000
-meryl memory=$mem union-sum output $output_meryl $meryl_dbs
-```
-meryl will try to make 64 x 2 files per meryl dbs to merge.
-
-## 3. Histogram
-What’s in my meryl db?
-This will give you a short summary of the k-mers, unique / distinct / total.
-
-```
-meryl statistics $output_meryl | head
-```
-
-Without the head, the histogram is printed after the summary, which could go very long.
-
-Get the histogram: This gives a traditional 2-column histogram, ready for genomescope or any other tool.
-
-```
-meryl histogram $output_meryl > $output_meryl.hist
-```
-
-Ploidy estimation including erroneous k-mer boundaries can be made by this script:
-```
-Java -jar -Xmx256m /path/to/this/meryl-accessories/scripts/kmerHistToPloidyDepth.jar $output_meryl.hist > $output_meryl.hist.ploidy
-```
-
-The output is a tdf file, with
-```
-Ploidy	Depth	Boundary
-```
-
-Depth is the depth where we see a ‘peak’ for ploidy > 0.
-Boundaries are the dips in the histogram.
-
-# 2. Copy-number comparison (spectra-cn)
-This script is the meryl version spectra-cn plot, introduced and implemented by [KAT](https://github.com/TGAC/KAT).
-The scripts here provide a way to draw unstacked, stacked histograms by copy numbers or specific to assemblies. No dependency to KAT.
-
-## 1. Get kmers from the read set and assembly (assemblies)
-Use the above tricks for building the meryl db for the reads.
-For each assembly,
-```
-meryl count memory=8 output $meryl_db <asm.fasta>
-```
-Should work fine with most of the genomes. This is using 8G of memory (or lower), taking a few seconds to build the $meryl_db.
-
-## 2. Get assembly-specific and shared kmers
-When working with 2 genome assemblies,
-such as one primary and alternate haplotype assemblies from diploid genomes,
-or two haplotype assemblies generated with trio-binning,
-the interest will be to see how many kmers are over / under represented compared to the expected copy numbers.
-
-Here, we will get assembly-specific (private to one of the assemblies) kmers and the shared kmers in separate temporary meryl dbs for convenience.
-
-hap1 and hap2 can be set as
-
->hap1=paternal
-
->hap2=maternal
-
-Or
-
->hap1=pri
-
->hap2=alt
-
-
-```
-meryl difference output $name.${hap2}_only.meryl $name.${hap2}.meryl $name.${hap1}.meryl
-meryl difference output $name.${hap1}_only.meryl $name.${hap1}.meryl $name.${hap2}.meryl
-meryl intersect output $name.${hap1}_shrd.meryl $name.${hap1}.meryl $name.${hap2}.meryl
-meryl intersect output $name.${hap2}_shrd.meryl $name.${hap2}.meryl $name.${hap1}.meryl
-```
-
-This generates 4 meryl dbs; and we need one more that sums up all the kmer counts:
-```
-meryl union-sum output $name.${hap1}_${hap2}_shrd.meryl $name.${hap1}_only.meryl $name.${hap1}_shrd.meryl $name.${hap2}_only.meryl $name.${hap2}_shrd.meryl
-```
-
-## 3. Intersect with the read meryl db
-Now, intersect the above kmer set of interest with the kmers from the read set, and get the kmer counts.
-
-* 0-counts in the read set; i.e. only seen in the assembly.
-Most likely assembly errors or kmers difficult to get from illumina reads
-
-```
-meryl difference output $name.only.meryl $name.${hap1}_${hap2}_shrd.meryl $name.k21.meryl
-```
-
-This kmer set is a useful indicator of bp errors.
-The number of k-mers are associate-able with bp, so roughly the number of distinct kmers in this set are representing number of erroneous bases in the assembly.
-It is difficult to distinguish kmers not sequence-able with illumina reads though, so it might be useful for comparing overal bp error rate in different assemblies from the same individual.
-
-```
-meryl statistics $name.only.meryl | head
-```
-
-Switch the two inputs now to get:
-
-* 0-counts in the asm; i.e. only seen in the illumina reads
-```
-meryl difference output $name.k21.0.meryl $name.k21.meryl $name.${hap1}_${hap2}_shrd.meryl
-```
-
-* 1~4 copy kmers
-```
-for i in $(seq 1 4)
-do
-    meryl intersect output $name.k21.$i.meryl $name.k21.meryl [ equal-to $i $name.${hap1}_${hap2}_shrd.meryl ]
-done
-```
-
-* \>4 copy kmers
-```
-meryl intersect output $name.k21.gt$i.meryl $name.k21.meryl [ greater-than $i $name.${hap1}_${hap2}_shrd.meryl ]
-```
-
-## 4. Spectra-cn plots
-
-The final histogram file can be obtained with:
-```
-echo -e "Copies\tkmer_multiplicity\tCount" > $name.spectra-cn.hist
-meryl histogram $name.k21.0.meryl | awk '{print "illumina-only\t"$0}' >> $name.spectra-cn.hist
-for i in $(seq 1 4)
-do
-    meryl histogram $name.k21.$i.meryl | awk -v cn=$i '{print cn"\t"$0}' >> $name.spectra-cn.hist
-done
-meryl histogram $name.k21.gt$i.meryl | awk -v cn=">$i" '{print cn"\t"$0}' >> $name.spectra-cn.hist
-```
-
-## 5. Spectra-hap plots
-Since we are interested in comparing the portion of kmers each haplotype (or pseudo haplotype) assemblies have,
-let’s make some plots with kmers grouped by specific / shared kmers.
-
-```
-meryl intersect output $name.k21.$hap1.meryl $name.k21.meryl $name.${hap1}_only.meryl
-meryl intersect output $name.k21.$hap2.meryl $name.k21.meryl $name.${hap2}_only.meryl
-meryl intersect output $name.k21.shrd.meryl $name.k21.meryl $name.${hap1}_shrd.meryl
-```
-
-Again, get the histograms by groups.
-```
-echo -e "kmer\tkmer_multiplicity\tCount" > $name.spectra-hap.hist
-meryl histogram $name.k21.0.meryl | awk '{print "illumina-only\t"$0}' >> $name.spectra-hap.hist
-meryl histogram $name.k21.$hap1.meryl | awk -v hap="$hap1-only" '{print hap"\t"$0}' >> $name.spectra-hap.hist
-meryl histogram $name.k21.$hap2.meryl | awk -v hap="$hap2-only" '{print hap"\t"$0}' >> $name.spectra-hap.hist
-meryl histogram $name.k21.shrd.meryl | awk -v hap="shared" '{print hap"\t"$0}' >> $name.spectra-hap.hist
-```
-
-`spectracn.R` is an example to generate plots for `$name.spectra-hap.hist`. More instructions will be posted later.
-
-
-# 3. Haplotype specific mers for trio binning and making blob-plots
-
-`_submit_meryl2_build_hapmers.sh` does the binning.
-For making blob-plots, use the temporary scripts uploaded to [here]( https://github.com/arangrhie/TrioBinning/blob/master/hap_kmer_plot.R).
-(Update will be followed)
-
-# 4. Include or exclude read pairs having specific kmers in one of the reads
-`meryl-lookup` has a utility to include / exclude reads (or read pairs) containing specific kmers.
-
-
-One use-case is to exclude all read pairs containing unwanted haplotype reads.
-In this case, 
-we can exclude i.e. all the paternal reads from Hi-C reads for aligning or scaffolding with maternal reads only.
-
-For single-end reads:
-```
-# Include all reads having kmers in $meryl
-meryl-lookup -include -mers $meryl -sequence $read | pigz -c > $out.fastq.gz
-
-# Exclude all reads having kmers in $meryl
-meryl-lookup -exclude -mers $meryl -sequence $read | pigz -c > $out.fastq.gz
-```
-
-For paired end reads:
-```
-# Include all reads having kmers in $meryl
-meryl-lookup -include -mers $meryl -sequence $read1 -sequence2 $read2 -r2 $out.R2.fastq.gz | pigz -c > $out.R1.fastq.gz
-
-# Exclude all reads having kmers in $meryl
-meryl-lookup -exclude -mers $meryl -sequence $read1 -sequence2 $read2 -r2 $out.R2.fastq.gz | pigz -c > $out.R1.fastq.gz
-```
-
-`exclude_reads.sh` is a wrapper script to make it easy to filter out reads in the above use-case.
-```
-./exclude_reads.sh haplotype-Paternal.filt.meryl R1.fastq.gz R2.fastq.gz mygenome.mat > mygenome.mat.log
-```
-will generate `mygenome.mat.R1.fastq.gz` and `mygenome.mat.R2.fastq.gz`.
diff --git a/scripts/_submit_cn.sh b/scripts/_submit_cn.sh
deleted file mode 100755
index 9cbc357..0000000
--- a/scripts/_submit_cn.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#! /bin/bash
-
-if [[ "$#" -lt 3 ]]; then
-	echo "Usage: ./_submit_cn.sh <read-db.meryl> <k> <asm1.fasta> [asm2.fasta] <out>"
-	exit -1
-fi
-
-readdb=$1
-k=$2
-asm1=$3
-asm2=$4
-out=$5
-
-args="$readdb $k $asm1 $asm2 $out"
-if [ -z $out ]; then
-	out="$asm2"
-	args="$readdb $k $asm1 $out"
-fi
-
-cpus=32
-mem=48g
-name=$out.spectra-cn
-script="$tools/meryl/scripts/eval/spectra-cn.sh"
-partition=quick
-walltime=4:00:00
-path=`pwd`
-
-mkdir -p logs
-log=logs/$name.%A.log
-
-echo "\
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args"
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args 
diff --git a/scripts/_submit_cn_hap.sh b/scripts/_submit_cn_hap.sh
deleted file mode 100755
index 67beb69..0000000
--- a/scripts/_submit_cn_hap.sh
+++ /dev/null
@@ -1,104 +0,0 @@
-#! /bin/bash
-
-if [[ "$#" -lt 5 ]]; then
-	echo "Usage: ./_submit_cn_hap.sh <read-db.meryl> <hap1.meryl> <hap2.meryl> <k> <asm1.fasta> [asm2.fasta] <out>"
-	exit -1
-fi
-
-readdb=$1
-hap1=$2
-hap2=$3
-k=$4
-asm1=$5
-asm2=$6
-out=$7
-
-if [ -z $out ]; then
-	out=$6
-	asm2=""
-fi
-
-mkdir -p logs
-# All jobs are expected to finish within 4 hours
-partition=quick
-walltime=4:00:00
-path=`pwd`
-extra=""
-
-#### Get spectra-cn plots and QV stats
-cpus=32
-mem=48g
-name=$out.spectra-cn
-script="$tools/meryl/scripts/eval/spectra-cn.sh"
-args="$readdb $k $asm1 $asm2 $out"
-log=logs/$name.%A.log
-
-echo "\
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args"
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args > cn.jid
-jid=`cat cn.jid`
-
-#### Get blob plots
-cpus=8
-mem=10g
-
-script="$tools/meryl/scripts/trio/hap_blob.sh"
-# ./hap_blob.sh <hap1.meryl> <hap2.meryl> <asm1.fasta> [asm2.fasta] <out>
-args="$hap1 $hap2 $asm1 $asm2 $out"
-name=$out.blob
-log=logs/$name.%A.log
-
-echo "\
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args"
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args > blob.jid
-
-
-#### Get haplotype specfic spectra-cn plots
-cpus=24
-mem=10g
-extra="--dependency=afterok:$jid"	# Re-uses asm.meryl dbs in spectra-cn.sh.
-
-name=$out.spectra-hap
-script="$tools/meryl/scripts/trio/spectra-hap.sh"
-args="$readdb $hap1 $hap2 $k $asm1 $asm2 $out"
-log=logs/$name.%A.log
-
-echo "\
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args"
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args > hap.jid
-
-#### Get phase blocks
-cpus=12
-mem=72g
-extra=""
-
-script="$tools/meryl/scripts/trio/phase_block.sh"
-# ./phase_block.sh <asm.fasta> <mat.meryl> <pat.meryl> <out>
-
-
-if [[ "$asm2" == "" ]] ; then
-	# Only one assembly given.
-	args="$asm1 $hap1 $hap2 $out"
-        name=$out.phase-block
-else
-	args="$asm1 $hap1 $hap2 $out.${asm1/.fasta/}"
-	name=$out.phase-block.${asm1/.fasta/}
-fi
-log=logs/$name.%A.log
-
-echo "\
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args"
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args > block1.jid
-
-if [[ "$asm2" == "" ]] ; then
-	exit 0
-fi
-
-args="$asm2 $hap1 $hap2 $out.${asm2/.fasta/}"
-name=$out.phase-block.${asm2/.fasta/}
-log=logs/$name.%A.log
-
-echo "\
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args"
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args > block2.jid
-
diff --git a/scripts/_submit_meryl2_build.sh b/scripts/_submit_meryl2_build.sh
deleted file mode 100755
index 9091f2e..0000000
--- a/scripts/_submit_meryl2_build.sh
+++ /dev/null
@@ -1,161 +0,0 @@
-#!/bin/bash
-
-# meryl_count=/path/to/meryl/scripts/meryl_count/
-meryl_count=$tools/meryl/scripts/meryl_count
-
-if [ -z $1 ]; then
-    echo "Usage: ./_submit_meryl2_build.sh <k-size> <input.fofn> <out_prefix> [mem=T]"
-    echo -e "\t<k-size>: kmer size k"
-    echo -e "\t<input.fofn>: ls *.fastq.gz > input.fofn. accepts fasta, fastq, gzipped or not."
-    echo -e "\t<out_prefix>: Final merged meryl db will be named as <out_prefix>.meryl"
-    echo -e "\t[mem=T]: Submit memory option on sbatch [DEFAULT=TRUE]. Set it to F to turn it off."
-    exit -1
-fi
-
-k=$1
-input_fofn=$2
-out_prefix=$3
-mem_opt=$4
-
-
-LEN=`wc -l $input_fofn | awk '{print $1}'`
-
-mkdir -p logs
-
-# Split files when >12GB
-cpus=20
-if [[ "$mem_opt" = "F" ]]; then
-        mem=""
-else
-        mem="--mem=4g"
-fi
-name=$out_prefix.split
-script=$meryl_count/split.sh
-partition=quick
-walltime=4:00:00
-path=`pwd`
-log=logs/$name.%A_%a.log
-
-wait_for=""
-split=0
-
-split_arrs=""
-
-for i in $(seq 1 $LEN)
-do
-	fq=`sed -n ${i}p $input_fofn`
-	GB=`du -k $fq  | awk '{printf "%.0f", $1/1024/1024}'`
-	if [[ $GB -lt 12 ]]; then
-	    echo "$fq is $GB, less than 12GB. Skip splitting."
-	    echo $fq >> $input_fofn.$i
-	else
-	    echo "$fq is $GB, over 12GB. Will split and run meryl in parallel."
-	    echo "Split files will be in $input_fofn.$i"
-	    args="$input_fofn"
-	    split_arrs="$split_arrs$i,"
-	    wait_for="${wait_for}afterok:$split_jid,"
-	    split=1
-	    echo
-	fi
-done
-
-if [ $split -eq 1 ]; then
-	split_arrs=${split_arrs%,}
-	echo "
-	sbatch -D $path -J $name --array=$split_arrs --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime --error=$log --output=$log $script $args"
-        sbatch -D $path -J $name --array=$split_arrs --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime --error=$log --output=$log $script $args | awk '{print $NF}' > split_jid
-	split_jid=`cat split_jid`
-	wait_for="afterok:$split_jid"
-	cpus=2
-	if [[ "$mem_opt" = "F" ]]; then
-	        mem=""
-	else
-        	mem="--mem=1g"
-	fi
-	name=$out_prefix.concat
-	script=$meryl_count/concat_splits.sh
-	args="$k $input_fofn $out_prefix"
-	partition=quick
-	walltime=10:00
-	path=`pwd`
-	log=logs/$name.%A.log
-	wait_for="--dependency=${wait_for%,}"
-	echo "
-	sbatch -D $path -J $name --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime $wait_for --error=$log --output=$log $script $args"
-	sbatch -D $path -J $name --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime $wait_for --error=$log --output=$log $script $args
-	exit 0
-else
-	rm $input_fofn.*
-	wait_for=""
-fi
-
-offset=$((LEN/1000))
-leftovers=$((LEN%1000))
-
-cpus=32 # Max: 64 per each .meryl/ file writer
-if [[ "$mem_opt" = "F" ]]; then
-	mem=""
-else
-	mem="--mem=40g"
-fi
-name=$out_prefix.count
-script=$meryl_count/meryl2_count.sh
-partition=quick
-walltime=4:00:00
-path=`pwd`
-log=logs/$name.%A_%a.log
-
-if [ -e meryl_count.jid ]; then
-    echo "Removing meryl_count.jid"
-    cat meryl_count.jid
-    rm meryl_count.jid
-fi
-
-for i in $(seq 0 $offset)
-do
-    args="$k $input_fofn $i"
-    if [[ $i -eq $offset ]]; then
-        arr_max=$leftovers
-    else
-        arr_max=1000
-    fi
-    echo "\
-    sbatch -J $name $mem --partition=$partition --cpus-per-task=$cpus -D $path --array=1-$arr_max --time=$walltime --error=$log --output=$log $script $args"
-    sbatch -J $name $mem --partition=$partition --cpus-per-task=$cpus -D $path --array=1-$arr_max --time=$walltime --error=$log --output=$log $script $args | awk '{print $NF}' >> meryl_count.jid
-done
-
-# Wait for these jobs
-WAIT="afterok:"`cat meryl_count.jid | tr '\n' ',afterok:'`
-WAIT=${WAIT%,}
-
-## Collect .meryl list
-if [ -e  meryl_count.meryl.list ]; then
-    echo "Removing meryl_count.meryl.list"
-    cat meryl_count.meryl.list
-    rm  meryl_count.meryl.list
-fi
-
-for line_num in $(seq 1 $LEN)
-do
-    input=`sed -n ${line_num}p $input_fofn`
-    name=`echo $input | sed 's/.fastq.gz$//g' | sed 's/.fq.gz$//g' | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
-    name=`basename $name`
-    echo "$name.$k.$line_num.meryl" >> meryl_count.meryl.list
-done
-
-cpus=48 # Max: 64 per each .meryl/ file writer
-if [[ "$mem_opt" = "F" ]]; then
-        mem=""
-else
-        mem="--mem=32g"
-fi
-walltime=4:00:00
-partition=norm
-name=$out_prefix.union_sum
-script=$meryl_count/meryl2_union_sum.sh
-log=logs/$name.%A.log
-args="$k meryl_count.meryl.list $out_prefix"
-echo "\
-sbatch -J $name $mem --partition=$partition --cpus-per-task=$cpus -D $path --dependency=$WAIT --time=$walltime --error=$log --output=$log $script $args"
-sbatch -J $name $mem --partition=$partition --cpus-per-task=$cpus -D $path --dependency=$WAIT --time=$walltime --error=$log --output=$log $script $args | awk '{print $NF}' > meryl_union_sum.jid
-
diff --git a/scripts/_submit_meryl2_build_10x.sh b/scripts/_submit_meryl2_build_10x.sh
deleted file mode 100755
index 05a6df8..0000000
--- a/scripts/_submit_meryl2_build_10x.sh
+++ /dev/null
@@ -1,105 +0,0 @@
-#!/bin/bash
-
-# meryl_count=/path/to/meryl/scripts/meryl_count/
-meryl_count=$tools/meryl/scripts/meryl_count
-
-if [ -z $1 ]; then
-    echo "Usage: ./_submit_meryl2_build.sh <k-size> <R1.fofn> <R2.fofn> <out_prefix> [mem=T]"
-    echo -e "\t<k-size>: kmer size k"
-    echo -e "\t<R1.fofn>: Read 1. The first 23 bases will get stripped off."
-    echo -e "\t<R2.fofn>: Read 2. Will be processed as normal."
-    echo -e "\t<out_prefix>: Final merged meryl db will be named as <out_prefix>.meryl"
-    echo -e "\t[mem=T]: Submit memory option on sbatch [DEFAULT=TRUE]. Set it to F to turn it off."
-    exit -1
-fi
-
-k=$1
-R1=$2
-R2=$3
-out_prefix=$4
-mem_opt=$5
-
-mkdir -p logs
-
-# Split files >10GB
-cpus=20
-if [[ "$mem_opt" = "F" ]]; then
-	mem=""
-else
-	mem="--mem=4g"
-fi
-name=$out_prefix.split
-partition=quick
-walltime=4:00:00
-path=`pwd`
-log=logs/$name.%A_%a.log
-
-wait_for=""
-split=0
-
-script=$meryl_count/split_10x.sh
-LEN=`wc -l $R1 | awk '{print $1}'`
-
-echo "R1 will be split to trim off the barcodes."
-split_arrs="1-$LEN"
-args="$R1"
-echo "
-sbatch -D $path -J $name --array=$split_arrs --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime --error=$log --output=$log $script $args"
-sbatch -D $path -J $name --array=$split_arrs --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime --error=$log --output=$log $script $args | awk '{print $NF}' > split_jid
-split_jid=`cat split_jid`
-wait_for="${wait_for}afterok:$split_jid,"
-
-
-#####
-echo "$R2 will be split if >12G"
-
-script=$meryl_count/split.sh
-LEN2=`wc -l $R2 | awk '{print $1}'`
-
-split_arrs=""
-
-for i in $(seq 1 $LEN2)
-do
-        fq=`sed -n ${i}p $R2`
-        GB=`du -k $fq  | awk '{printf "%.0f", $1/1024/1024}'`
-        if [[ $GB -lt 12 ]]; then
-            echo "$fq is $GB, less than 12GB. Skip splitting."
-            echo $fq >> $R2.$i
-        else
-            echo "$fq is $GB, over 12GB. Will split and run meryl in parallel. Split files will be in $R2.$i"
-	    split_arrs="$split_arrs$i," # keep the line nums $i to split
-            split=1
-            echo
-        fi
-done
-
-if [[ $split -eq 1 ]]; then
-        split_arrs=${split_arrs%,}
-	args="$R2"
-        echo "
-        sbatch -D $path -J $name --array=$split_arrs --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime --error=$log --output=$log $script $args"
-        sbatch -D $path -J $name --array=$split_arrs --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime --error=$log --output=$log $script $args | awk '{print $NF}' >> split_jid
-        split_jid=`cat split_jid | tail -n1`
-        wait_for="${wait_for}afterok:$split_jid,"
-fi
-
-
-cpus=2
-if [[ "$mem_opt" = "F" ]]; then
-        mem=""
-else
-        mem="--mem=1g"
-fi
-name=$out_prefix.concat
-script=$meryl_count/concat_splits.sh
-args="$k $R1 $out_prefix $R2"
-partition=quick
-walltime=10:00
-path=`pwd`
-log=logs/$name.%A.log
-wait_for="--dependency=${wait_for%,}"
-echo "$wait_for"
-echo "
-sbatch -D $path -J $name --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime $wait_for --error=$log --output=$log $script $args"
-sbatch -D $path -J $name --partition=$partition $mem --cpus-per-task=$cpus --time=$walltime $wait_for --error=$log --output=$log $script $args
-
diff --git a/scripts/_submit_meryl2_build_hapmers.sh b/scripts/_submit_meryl2_build_hapmers.sh
deleted file mode 100755
index 4ca3a22..0000000
--- a/scripts/_submit_meryl2_build_hapmers.sh
+++ /dev/null
@@ -1,135 +0,0 @@
-#!/bin/bash
-
-# build=/path/to/codes/and/scripts/
-build=$tools/meryl/scripts/build
-
-if [ -z $1 ]; then
-    echo "Usage: ./_submit_meryl2_build_hapmers.sh <k-size> <hap1.fofn> <hap2.fofn>"
-    echo -e "\t<k-size>: kmer size k"
-    echo -e "\t<hap1.fofn>: ls *.fastq.gz > hap1.fofn. accepts fasta, fastq, gzipped or not."
-    echo -e "\t<hap2.fofn>: ls *.fastq.gz > hap2.fofn. accepts fasta, fastq, gzipped or not."
-    echo -e "\tIntermediate kmer dbs will be named after hap1 and hap2"
-    exit -1
-fi
-
-k=$1
-hap1_fofn=$2
-hap2_fofn=$3
-
-hap1=${hap1_fofn/.fofn/}
-hap2=${hap2_fofn/.fofn/}
-
-if [ -e build.jid ]; then
-    echo "Removing build.jid"
-    cat build.jid
-    rm build.jid
-fi
-
-# Build for hap1
-for hap in "$hap1" "$hap2"
-do
-	input_fofn=$hap.fofn
-	echo $input_fofn
-	
-	LEN=`wc -l $input_fofn | awk '{print $1}'`
-	offset=$((LEN/1000))
-	leftovers=$((LEN%1000))
-
-	mkdir -p logs
-
-	cpus=32 # Max: 64 per each .meryl/ file writer
-	mem=48g
-	name=build
-	script=$build/meryl2_count.sh
-	partition=norm
-	walltime=1-0
-	path=`pwd`
-	log=logs/$name.%A_%a.log
-
-	for i in $(seq 0 $offset)
-	do
-	    args="$k $input_fofn $i"
-	    if [[ $i -eq $offset ]]; then
-		arr_max=$leftovers
-	    else
-		arr_max=1000
-	    fi
-	    echo "\
-	    sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --array=1-$arr_max --time=$walltime --error=$log --output=$log $script $args"
-	    sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --array=1-$arr_max --time=$walltime --error=$log --output=$log $script $args >> build.jid
-	done
-
-
-	# Wait for these jobs
-	WAIT="afterok:"
-
-	job_nums=`wc -l build.jid | awk '{print $1}'`
-
-	if [[ $job_nums -eq 1 ]]; then
-	   jid=`cat build.jid`
-	   WAIT=$WAIT$jid
-	else
-
-	for jid in $(cat build.jid)
-	do
-	    WAIT=$WAIT$jid","
-	done
-	fi
-
-	## Collect .meryl list
-	if [ -e  build.$hap.meryl.list ]; then
-	    echo "Removing build.meryl.list"
-	    cat build.$hap.meryl.list
-	    rm  build.$hap.meryl.list
-	fi
-
-	for line_num in $(seq 1 $LEN)
-	do
-	    input=`sed -n ${line_num}p $input_fofn`
-	    name=`echo $input | sed 's/.fastq.gz$//g' | sed 's/.fq.gz$//g' | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
-	    name=`basename $name`
-	    echo "$name.$k.$line_num.meryl" >> build.$hap.meryl.list
-	done
-
-	cpus=48 # Max: 64 per each .meryl/ file writer
-	mem=72g
-	name=meryl_union_sum
-	script=$build/meryl2_union_sum.sh
-	args="$k build.$hap.meryl.list $hap"
-	log=logs/$name.%A_%a.log
-
-	echo "\
-	sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path --dependency=$WAIT --time=$walltime --error=$log --output=$log $script $args"
-	sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path --dependency=$WAIT --time=$walltime --error=$log --output=$log $script $args > meryl_union_sum.jid
-done
-
-# Wait for these jobs
-WAIT="afterok:"
-
-job_id=meryl_union_sum.jid
-job_nums=`wc -l $job_id | awk '{print $1}'`
-
-if [[ $job_nums -eq 1 ]]; then
-   jid=`cat $job_jid`
-   WAIT=$WAIT$jid
-else
-
-for jid in $(cat build.jid)
-do
-    WAIT=$WAIT$jid","
-done
-fi
-
-cpus=48 # Max: 64 per each .meryl/ file writer
-mem=20g
-name=meryl_diff
-script=$build/meryl2_diff.sh
-args="$hap1.meryl $hap2.meryl"
-log=logs/$name.%A_%a.log
-partition=quick
-
-echo "\
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path --dependency=$WAIT --time=$walltime --error=$log --output=$log $script $args"
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path --dependency=$WAIT --time=$walltime --error=$log --output=$log $script $args > meryl_diff.jid
-
-
diff --git a/scripts/_submit_split.sh b/scripts/_submit_split.sh
deleted file mode 100755
index b65612c..0000000
--- a/scripts/_submit_split.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#! /bin/bash
-
-echo "Usage: ./_submit_split.sh <input.fofn>"
-echo "Split the input.fofn if >8GB"
-
-if [ -z $1 ]; then
-	echo "No input.fofn provided. Exit."
-	exit -1
-fi
-
-LEN=`wc -l $1 | awk '{print $1}'`
-
-cpus=6
-mem=4g
-name=split
-script=$tools/meryl/scripts/meryl_count/split.sh
-args=$1
-partition=norm
-walltime=1-0
-path=`pwd`
-extra="--array=1-$LEN"
-
-mkdir -p logs
-if [ -z $extra ]; then
-	log=logs/$name.%A.log
-else
-	log=logs/$name.%A_%a.log
-fi
-
-echo "\
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args"
-sbatch -J $name --mem=$mem --partition=$partition --cpus-per-task=$cpus -D $path $extra --time=$walltime --error=$log --output=$log $script $args
-
diff --git a/scripts/build/concat_splits.sh b/scripts/build/concat_splits.sh
deleted file mode 100755
index 2d61c13..0000000
--- a/scripts/build/concat_splits.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-
-echo "Usage: ./concat_splits.sh <k-size> <input.fofn> <out_prefix> [input2.fofn]"
-echo "[input2.fofn]: Only needed for 10X data"
-
-k=$1
-input_fofn=$2
-out_prefix=$3
-input2_fofn=$4
-
-if [[ -z $input_fofn ]] ; then
-	echo "No <input.fofn> given. Exit."
-	exit -1
-fi
-
-cat $input_fofn.* > $input_fofn.splits
-if [[ ! -z $input2_fofn ]]; then
-	cat $input2_fofn.* >> $input_fofn.splits
-fi
-
-echo "
-$tools/meryl/scripts/_submit_meryl2_build.sh $k $input_fofn.splits $out_prefix"
-$tools/meryl/scripts/_submit_meryl2_build.sh $k $input_fofn.splits $out_prefix
diff --git a/scripts/build/kmerHistToPloidyDepth.jar b/scripts/build/kmerHistToPloidyDepth.jar
deleted file mode 100755
index 6cacb89ebccaaabc24d766b75fc4f947bb9d9420..0000000000000000000000000000000000000000
GIT binary patch
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z0sU|0T^3=?`BdJY>oLKjv86?EKgZe??U^AN%P*hFn5V@r@Y|_dAVg~MzCgz&H(d*d
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z<Wq(~hZ~^+Tt^)Rcq2>!ok)bdml<>-5dusEGC_e48&Ab|J`uX9$UD(MD{B#;5ZEmy
z!c>qFWJ5uv8S=t-(A)?Da0;Uu3Lp9f4f!H%X+t&<w4fe&X)tI(Jp!DUB4{EuCn7Hl
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diff --git a/scripts/build/meryl2_count.sh b/scripts/build/meryl2_count.sh
deleted file mode 100755
index e12c812..0000000
--- a/scripts/build/meryl2_count.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/bash
-
-
-if [[ -z $1 ]] || [[ -z $2 ]]; then
-    echo "Usage: ./meryl2_count.sh <k> <input.fofn> [offset line_num]"
-    echo -e "\t<k>: k-size mers will be collected. REQUIRED."
-    echo -e "\t<input.fofn>: list of fastq / fasta file. REQUIRED."
-    echo -e "\t[offset]: OPTIONAL. DEFAULT=0. For array job limit only."
-    echo -e "\t[line_num]: OPTIONAL. (offset * 1000 + line_num)'th line of input.fofn will be the input."
-    echo -e "\t\t\$SLURM_ARRAY_TASK_ID will be used if not specified."
-    exit -1
-fi
-
-k=$1
-input_fofn=$2
-
-
-if [ -z $3 ]; then
-    offset=0
-else
-    offset=$3
-fi
-
-if [ ! -z $4 ]; then
-    line_num=$4
-else
-    line_num=$SLURM_ARRAY_TASK_ID
-fi
-
-#  Note: Provide memory in Gb unit. SLURM provides $SLURM_MEM_PER_NODE in Mb.
-#            Give extra 4Gb to avoid 'Bus Error' form running out of memory.
-if [[ -z $SLURM_MEM_PER_NODE ]]; then
-	mem=32
-else
-	mem=$(((SLURM_MEM_PER_NODE/1024)-4))
-fi
-line_num=$(((offset * 1000) + $line_num))
-
-# Read in the input path
-input=`sed -n ${line_num}p $input_fofn`
-
-# Name it accordingly
-name=`echo $input | sed 's/.fastq.gz$//g' | sed 's/.fq.gz$//g' | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
-name=`basename $name`
-
-output=$name.$k.$line_num.meryl
-
-if [ ! -d $output ]; then
-    # Run meryl count: Collect k-mer frequencies
-    echo "
-    meryl k=$k memory=$mem count $input output $output
-    "
-    meryl k=$k memory=$mem count $input output $output
-else
-    echo "$output dir already exist. Nothing to do with $name."
-fi
-
-
diff --git a/scripts/build/meryl2_count_10x.sh b/scripts/build/meryl2_count_10x.sh
deleted file mode 100755
index 94d0f4a..0000000
--- a/scripts/build/meryl2_count_10x.sh
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/bin/bash
-
-
-if [[ -z $1 ]] || [[ -z $2 ]]; then
-    echo "Usage: ./meryl2_count.sh <k> <input.fofn> [offset line_num]"
-    echo -e "\t<k>: k-size mers will be collected. REQUIRED."
-    echo -e "\t<input.fofn>: list of fastq.gz file. Read pair 1 from 10X reads. REQUIRED."
-    echo -e "\t[offset]: OPTIONAL. DEFAULT=0. For array job limit only."
-    echo -e "\t[line_num]: OPTIONAL. (offset * 1000 + line_num)'th line of input.fofn will be the input."
-    echo -e "\t\t\$SLURM_ARRAY_TASK_ID will be used if not specified."
-    echo -e "\t*NOTE* This script is trimming off the first 23 bases before kmer counting. Only useful for 10X barcode trimming."
-    exit -1
-fi
-
-k=$1
-input_fofn=$2
-
-
-if [ -z $3 ]; then
-    offset=0
-else
-    offset=$3
-fi
-
-if [ ! -z $4 ]; then
-    line_num=$4
-else
-    line_num=$SLURM_ARRAY_TASK_ID
-fi
-
-#  Note: Provide memory in Gb unit. SLURM provides $SLURM_MEM_PER_NODE in Mb.
-#            Give extra 4Gb to avoid 'Bus Error' form running out of memory.
-mem=$(((SLURM_MEM_PER_NODE/1024)-4))
-line_num=$(((offset * 1000) + $line_num))
-
-# Read in the input path
-input=`sed -n ${line_num}p $input_fofn`
-
-# Name it accordingly
-name=`echo $input | sed 's/.fastq.gz$//g' | sed 's/.fq.gz$//g' | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
-name=`basename $name`
-
-output=$name.$k.$line_num.meryl
-
-if [ ! -d $output ]; then
-    # Run meryl count: Collect k-mer frequencies
-    echo "
-    zcat $input | awk '{if (NR%2==1) {print $1} else {print substr($1,24)}}' | meryl k=$k threads=$SLURM_CPUS_PER_TASK memory=$mem count output $output -
-    "
-    zcat $input | awk '{if (NR%2==1) {print $1} else {print substr($1,24)}}' | meryl k=$k threads=$SLURM_CPUS_PER_TASK memory=$mem count output $output -
-else
-    echo "$output dir already exist. Nothing to do with $name."
-fi
-
-
diff --git a/scripts/build/meryl2_diff.sh b/scripts/build/meryl2_diff.sh
deleted file mode 100755
index 9d0f33a..0000000
--- a/scripts/build/meryl2_diff.sh
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/bin/bash
-
-if [[ -z $1 ]] || [[ -z $2 ]]; then
-	echo "Usage: meryl2_diff.sh <db1.meryl> <db2.meryl>"
-	exit -1
-fi
-
-db1=$1
-db2=$2
-
-db1=${db1/.meryl/}
-db2=${db2/.meryl/}
-
-if [ ! -d ${db1}_only.meryl ]; then
-	echo "\
-	meryl difference output ${db1}_only.meryl $db1.meryl $db2.meryl"
-	meryl difference output ${db1}_only.meryl $db1.meryl $db2.meryl
-	echo
-fi
-
-if [ ! -d ${db2}_only.meryl ]; then
-	echo "\
-	meryl difference output ${db2}_only.meryl $db2.meryl $db1.meryl"
-	meryl difference output ${db2}_only.meryl $db2.meryl $db1.meryl
-	echo
-fi
-
-echo "
-sh $tools/TrioBinning/meryl_count/meryl2_filt.sh ${db1}_only.meryl"
-sh $tools/TrioBinning/meryl_count/meryl2_filt.sh ${db1}_only.meryl
-
-echo "
-sh $tools/TrioBinning/meryl_count/meryl2_filt.sh ${db2}_only.meryl"
-sh $tools/TrioBinning/meryl_count/meryl2_filt.sh ${db2}_only.meryl
-
diff --git a/scripts/build/meryl2_filt.sh b/scripts/build/meryl2_filt.sh
deleted file mode 100755
index b8ef081..0000000
--- a/scripts/build/meryl2_filt.sh
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/bin/bash
-
-if [ -z $1 ]; then
-	echo "Usage: ./meryl2_filt.sh <in.meryl>"
-	exit -1
-fi
-
-db=$1
-db=${db/.meryl/}
-
-echo "Generate $db.hist"
-meryl histogram $db.meryl > $db.hist
-
-echo "
-java -jar -Xmx1g $tools/TrioBinning/meryl_count/kmerHistToPloidyDepth.jar $db.hist
-"
-java -jar -Xmx1g $tools/TrioBinning/meryl_count/kmerHistToPloidyDepth.jar $db.hist > $db.hist.ploidy
-
-cat $db.hist.ploidy
-
-filt=`sed -n 2p $db.hist.ploidy | awk '{print $NF}'`
-
-echo "Filter out kmers <= $filt"
-
-echo "
-meryl greater-than $filt output $db.gt$filt.meryl $db.meryl
-"
-meryl greater-than $filt output $db.gt$filt.meryl $db.meryl
-
-
diff --git a/scripts/build/meryl2_hapmers.sh b/scripts/build/meryl2_hapmers.sh
deleted file mode 100755
index 728e84a..0000000
--- a/scripts/build/meryl2_hapmers.sh
+++ /dev/null
@@ -1,79 +0,0 @@
-#!/bin/sh
-
-if [[ -z $1 ]] || [[ -z $2 ]] || [[ -z $3 ]] || [[ -z $4 ]]; then
-    echo "Usage: ./meryl_count_asm.sh <hapA.mcdat> <hapB.mcdat> <asmA.fasta> <asmB.fasta>"
-    exit -1
-fi
-
-hap_a=$1	# meryl hap_a.mcdat
-hap_b=$2	# meryl hap_b.mcdat
-
-a_fa=$3		# hap_a.fasta
-b_fa=$4		# hap_b.fasta
-
-hap_a=${hap_a/.mcdat/}
-hap_b=${hap_b/.mcdat/}
-
-a_name=`echo $a_fa | sed 's/.fasta$//g' | sed 's/.fa$//g'`
-b_name=`echo $b_fa | sed 's/.fasta$//g' | sed 's/.fa$//g'`
-
-echo "Generate qr dbs"
-if ! [ -s $hap_a.qr ]; then
-echo "\
-simple-dump -m 21 -s $hap_a -e $hap_a.qr"
-simple-dump -m 21 -s $hap_a -e $hap_a.qr
-echo
-fi
-
-if ! [ -s $hap_b.qr ]; then
-echo "\
-simple-dump -m 21 -s $hap_b -e $hap_b.qr"
-simple-dump -m 21 -s $hap_b -e $hap_b.qr
-echo
-fi
-
-echo "Start counting"
-if ! [ -s ${a_name}"_"$hap_a.counts ]; then
-echo "\
-simple-dump -m 21 -e $hap_a.qr -f $a_fa | awk -v name=$a_name \'{print name\\t\$0}\' > ${a_name}_$hap_a.counts"
-simple-dump -m 21 -e $hap_a.qr -f $a_fa | awk -v name=$a_name '{print name"\t"$0}'   > ${a_name}"_"$hap_a.counts
-echo
-fi
-
-if ! [ -s ${b_name}"_"$hap_a.counts ]; then
-echo "\
-simple-dump -m 21 -e $hap_a.qr -f $b_fa | awk -v name=$b_name \'{print name\\t\$0}\' > ${b_name}_$hap_a.counts"
-simple-dump -m 21 -e $hap_a.qr -f $b_fa | awk -v name=$b_name '{print name"\t"$0}'   > ${b_name}"_"$hap_a.counts
-echo
-fi
-
-if ! [ -s ${a_name}"_"$hap_b.counts ]; then
-echo "\
-simple-dump -m 21 -e $hap_b.qr -f $a_fa | awk -v name=$a_name \'{print name\\t\$0}\' > ${a_name}"_"$hap_b.counts"
-simple-dump -m 21 -e $hap_b.qr -f $a_fa | awk -v name=$a_name '{print name"\t"$0}'   > ${a_name}"_"$hap_b.counts
-echo
-fi
-
-if ! [ -s ${b_name}"_"$hap_b.counts ]; then
-echo "\
-simple-dump -m 21 -e $hap_b.qr -f $b_fa | awk -v name=$b_name \'{print name\\t\$0}\' > ${b_name}"_"$hap_b.counts"
-simple-dump -m 21 -e $hap_b.qr -f $b_fa | awk -v name=$b_name '{print name"\t"$0}'   > ${b_name}"_"$hap_b.counts
-echo
-fi
-
-echo "Merge"
-echo "\
-paste ${a_name}_$hap_a.counts ${a_name}_$hap_b.counts > $a_name.counts"
-paste ${a_name}"_"$hap_a.counts ${a_name}"_"$hap_b.counts > $a_name.counts
-
-echo "\
-paste ${b_name}_$hap_a.counts ${b_name}_$hap_b.counts > $b_name.counts"
-paste ${b_name}"_"$hap_a.counts ${b_name}"_"$hap_b.counts > $b_name.counts
-
-echo "\
-echo -e "Assembly\tContig\t$hap_a\t$hap_b\tTotal" > hapmers.counts"
-echo -e "Assembly\tContig\t$hap_a\t$hap_b\tTotal" > hapmers.counts
-
-echo "\
-cat $a_name.counts $b_name.counts | awk '{print \$1\t\$2\t\$5\t\$NF\t\$3}' >> hapmers.counts"
-cat $a_name.counts $b_name.counts | awk '{print $1"\t"$2"\t"$5"\t"$NF"\t"$3}' >> hapmers.counts
diff --git a/scripts/build/meryl2_union_sum.sh b/scripts/build/meryl2_union_sum.sh
deleted file mode 100755
index 2a97d9f..0000000
--- a/scripts/build/meryl2_union_sum.sh
+++ /dev/null
@@ -1,119 +0,0 @@
-#!/bin/bash
-if [ -z $1 ]; then
-	echo "Usage: ./_meryl_union_sum.sh <k-size> <meryl.list> <output_prefix (no .meryl please)>"
-	echo -e "Merge <meryl.list>"
-	exit -1
-fi
-
-k=$1
-input_fofn=$2
-output_prefix=$3.k$k
-
-## Collect .meryl files
-LEN=`wc -l $input_fofn | awk '{print $1}'`
-NUM_DBS_TO_JOIN=100	# Join every $NUM_DBS_TO_JOIN as intermediates, then merge at the end
-JOIN_IDX=0
-
-echo "Set ulimit: ulimit -Sn 32000"
-ulimit -Sn 32000
-
-for FROM_IDX in $(seq 1 $NUM_DBS_TO_JOIN $LEN)
-do
-	END_IDX=$((FROM_IDX+$NUM_DBS_TO_JOIN-1))
-	if [ $END_IDX -gt $LEN ]; then
-	    END_IDX=$LEN
-	fi
-	meryl=""
-	for i in $(seq $FROM_IDX $END_IDX)
-	do
-	    input=`sed -n ${i}p $input_fofn`
-	    if [ -d $input ]; then
-        	meryl="$meryl $input"
-	    fi
-	done
-
-	echo "union-sum of $FROM_IDX - $END_IDX :"
-
-	JOIN_IDX=$((JOIN_IDX+1))
-	output=${output_prefix}.$JOIN_IDX
-	if [ ! -d $output ]; then
-	    echo "
-	    meryl \
-	        threads=$SLURM_CPUS_PER_TASK \
-	        memory=$((SLURM_MEM_PER_NODE/1024)) \
-	        k=$k \
-	        union-sum \
-	        output $output \
-	        $meryl
-	    "
-
-	    meryl \
-	        threads=$SLURM_CPUS_PER_TASK \
-	        memory=$((SLURM_MEM_PER_NODE/1024)) \
-	        k=$k \
-	        union-sum \
-	        output $output \
-	        $meryl
-	fi
-done
-
-if [ $JOIN_IDX -gt $NUM_DBS_TO_JOIN ]; then
-	echo -e "\tMore than $NUM_DBS_TO_JOIN intermediate files made."
-	echo -e "\tRe run meryl_union_sum.sh on $output_prefix.*.meryl."
-	exit 0
-fi
-
-if [ $JOIN_IDX -eq 1 ]; then
-	echo "All inputs merged to $output_prefix.1. Renaming to $output_prefix.meryl"
-	mv $output_prefix.1 $output_prefix.meryl
-	echo "Done!"
-	echo "
-	meryl histogram $output_prefix.meryl > $output_prefix.hist
-	"
-	meryl histogram $output_prefix.meryl > $output_prefix.hist
-
-	echo "Use $output_prefix.hist for genomescope etc."
-
-	echo "Cleaning up"
-	rm -r $meryl
-	exit 0
-fi
-
-meryl=""
-for i in $(seq 1 $JOIN_IDX)
-do
-    if [ -d $input ]; then
-        meryl="$meryl $output_prefix.$i"
-    fi
-done
-
-echo "union-sum of $output_prefix.[ 1 - $JOIN_IDX ] :"
-
-if [ ! -d $output_prefix ]; then
-    echo "
-    meryl \
-        threads=$SLURM_CPUS_PER_TASK \
-        memory=$((SLURM_MEM_PER_NODE/1024)) \
-        k=$k \
-        union-sum \
-        output $output_prefix.meryl \
-        $meryl
-    "
-
-    meryl \
-        threads=$SLURM_CPUS_PER_TASK \
-        memory=$((SLURM_MEM_PER_NODE/1024)) \
-        k=$k \
-        union-sum \
-        output $output_prefix.meryl \
-        $meryl
-fi
-
-echo "
-meryl histogram $output_prefix.meryl > $output_prefix.hist
-"
-meryl histogram $output_prefix.meryl > $output_prefix.hist
-
-echo "Use $output_prefix.hist for genomescope etc."
-
-echo "Done!"
diff --git a/scripts/build/split.sh b/scripts/build/split.sh
deleted file mode 100755
index d43dbbe..0000000
--- a/scripts/build/split.sh
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/bin/bash
-
-echo "Usage: ./split.sh <input.fofn> [LINE_NUM]"
-echo -e "\t<input.fofn>: fastq.gz files we want to split if > 8GB."
-echo -e "\t<input.fofn>.LINE_NUM will be generated."
-echo -e "\t\tUse it for next steps (trim or meryl_count)"
-echo
-
-FOFN=$1
-if [ -z $FOFN ]; then
-    echo "No <input.fofn> provided. Exit."
-    exit -1
-fi
-
-tid=$SLURM_ARRAY_TASK_ID
-LINE_NUM=$2
-
-if [ -z $tid ]; then
-    tid=$LINE_NUM
-fi
-
-if [ -z $tid ]; then
-    echo "No SLURM_ARRAY_TASK_ID or LINE_NUM provided. Exit."
-    exit -1
-fi
-
-cpus=$SLURM_CPUS_PER_TASK
-
-fq=`sed -n ${tid}p $FOFN`
-fq_prefix=`echo $fq | sed 's/.fastq.gz$//g' | sed 's/.fq.gz$//g' | sed 's/.fastq$//g' | sed 's/.fq$//g'`
-fq_prefix=`basename $fq_prefix`
-
-mkdir -p split
-
-echo "
-Splitting input file $fq"
-
-if [[ ${fq##*.} == "gz" ]]; then
-	echo "\
-	zcat $fq | split -a 4 -d -l 300000000 --additional-suffix=.fq   - split/$fq_prefix."
-	zcat $fq | split -a 4 -d -l 300000000 --additional-suffix=".fq" - split/$fq_prefix.
-else
-	echo "\
-	split -a 4 -d -l 300000000 --additional-suffix=.fq   $fq split/$fq_prefix."
-	split -a 4 -d -l 300000000 --additional-suffix=".fq" $fq split/$fq_prefix.
-fi
-
-echo "
-pigz --processes $cpus split/$fq_prefix.*.fq"
-pigz --processes $cpus split/$fq_prefix.*.fq
-
-ls split/$fq_prefix.[0-9][0-9][0-9][0-9].fq.gz > $FOFN.$tid
-LEN=`wc -l $FOFN.$tid | awk '{print $1}'`
-
-echo "Splitting done: $LEN files generated."
-
diff --git a/scripts/build/split_10x.sh b/scripts/build/split_10x.sh
deleted file mode 100755
index 2992720..0000000
--- a/scripts/build/split_10x.sh
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/bin/bash
-
-echo "Usage: ./split.sh <input.fofn> [LINE_NUM]"
-echo -e "\t<input.fofn>: fastq.gz files we want to split if > 8GB."
-echo -e "\t<input.fofn>.LINE_NUM will be generated."
-echo -e "\t\tUse it for next steps (trim or meryl_count)"
-echo
-
-FOFN=$1
-if [ -z $FOFN ]; then
-    echo "No <input.fofn> provided. Exit."
-    exit -1
-fi
-
-tid=$SLURM_ARRAY_TASK_ID
-LINE_NUM=$2
-
-if [ -z $tid ]; then
-    tid=$LINE_NUM
-fi
-
-if [ -z $tid ]; then
-    echo "No SLURM_ARRAY_TASK_ID or LINE_NUM provided. Exit."
-    exit -1
-fi
-
-cpus=$SLURM_CPUS_PER_TASK
-
-fq=`sed -n ${tid}p $FOFN`
-fq_prefix=`echo $fq | sed 's/.fastq.gz$//g' | sed 's/.fq.gz$//g' | sed 's/.fastq$//g' | sed 's/.fq$//g'`
-fq_prefix=`basename $fq_prefix`
-
-mkdir -p split
-
-echo "
-Strip off the first 23 basepairs (6 illumina library + 1 padding + 16 barcodes) and split the input file"
-
-if [[ ${fq##*.} == "gz" ]]; then
-	echo "\
-	zcat $fq | awk '{if (NR%2==1) {print \$1} else {print substr(\$1,24)}}' | split -a 4 -d -l 300000000 --additional-suffix=.fq - split/$fq_prefix."
-	zcat $fq | awk '{if (NR%2==1) {print $1} else {print substr($1,24)}}' | split -a 4 -d -l 300000000 --additional-suffix=".fq" - split/$fq_prefix.
-else
-	echo "\
-	cat $fq | awk '{if (NR%2==1) {print \$1} else {print substr(\$1,24)}}' | split -a 4 -d -l 300000000 --additional-suffix=.fq  - split/$fq_prefix."
-	cat $fq | awk '{if (NR%2==1) {print  $1} else {print substr($1,24)}}' | split -a 4 -d -l 300000000 --additional-suffix=".fq" - split/$fq_prefix.
-fi
-
-echo "
-pigz --processes $cpus split/$fq_prefix.*.fq"
-pigz --processes $cpus split/$fq_prefix.*.fq
-
-ls split/$fq_prefix.[0-9][0-9][0-9][0-9].fq.gz > $FOFN.$tid
-LEN=`wc -l $FOFN.$tid | awk '{print $1}'`
-
-echo "Splitting done: $LEN files generated."
-
diff --git a/scripts/cn_hap.sh b/scripts/cn_hap.sh
deleted file mode 100755
index 8c79ecb..0000000
--- a/scripts/cn_hap.sh
+++ /dev/null
@@ -1,62 +0,0 @@
-#! /bin/bash
-
-if [[ "$#" -lt 5 ]]; then
-	echo "Usage: ./cn_hap.sh <read-db.meryl> <hap1.meryl> <hap2.meryl> <k> <asm1.fasta> [asm2.fasta] <out>"
-	exit -1
-fi
-
-readdb=$1
-hap1=$2
-hap2=$3
-k=$4
-asm1=$5
-asm2=$6
-out=$7
-
-if [ -e $out ]; then
-        echo "$out already exists. Provide a different name. (Are we missing the <out>?)"
-        exit -1
-fi
-
-if [ -z $out ]; then
-	out=$6
-	asm2=""
-fi
-
-mkdir -p logs
-
-echo "
-Get spectra-cn plots and QV stats"
-name=$out.spectra-cn
-log=logs/$name.log
-nohup sh "$tools/meryl/scripts/eval"/spectra-cn.sh $readdb $k $asm1 $asm2 $out > $log
-
-echo "
-Get blob plots"
-name=$out.blob
-log=logs/$name.log
-nohup sh $tools/meryl/scripts/trio/hap_blob.sh $hap1 $hap2 $asm1 $asm2 $out > $log
-
-echo "
-Get haplotype specfic spectra-cn plots"
-name=$out.spectra-hap
-log=logs/$name.log
-nohup sh $tools/meryl/scripts/trio/spectra-hap.sh $readdb $hap1 $hap2 $k $asm1 $asm2 $out > $log
-
-echo "
-Get phase blocks"
-name=$out.phase-block
-log=logs/$name.log
-
-echo "
-For $asm1" > $log
-nohup sh $tools/meryl/scripts/trio/phase_block.sh $asm1 $hap1 $hap2 $out.${asm1/.fasta/}  >> $log
-
-if [ -z $asm2 ] ; then
-	exit 0
-fi
-
-echo "
-For $asm2" >> $log
-nohup sh $tools/meryl/scripts/trio/phase_block.sh $asm2 $hap1 $hap2 $out.${asm2/.fasta/}  >> $log
-
diff --git a/scripts/eval/bedCalcN50.jar b/scripts/eval/bedCalcN50.jar
deleted file mode 100755
index 440510f33bebc7f15028b904816ed79cc8ee225a..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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diff --git a/scripts/eval/spectra-cn.sh b/scripts/eval/spectra-cn.sh
deleted file mode 100755
index d80b6a2..0000000
--- a/scripts/eval/spectra-cn.sh
+++ /dev/null
@@ -1,225 +0,0 @@
-#!/bin/bash
-
-echo "Usage: ./spectra-cn.sh <read.meryl> <k> <asm1.fasta> [asm2.fasta] out-prefix"
-echo -e "\t<read.meryl>\t: Generated with meryl count from i.e. illumina wgs reads"
-echo -e "\t<k>\t: k-size used to build <read.meryl>"
-echo -e "\t<asm1.fasta>\t: haplotype 1 assembly. gzipped or not"
-echo -e "\t[asm2.fasta]\t: haplotype 2 assembly. gzipped or not"
-echo -e "\t<out-prefix>: output prefix. Required."
-echo
-echo -e "<asm1.spectra-cn> will be generated as output."
-echo -e "\tWhen asm2 and out-prefix are given,"
-echo -e "\t\t<asm2.spectra-cn> and"
-echo -e "\t\t<out-prefix>.spectra-hap.hist"
-echo -e "\twill be generated in addition."
-echo
-
-
-if [[ $# -lt 4  ]]; then
-    echo "No args provided. Exit."
-    exit -1
-fi
-
-if [ -z $scripts ]; then
-    echo "Setting \$scripts path"
-    scripts=`which meryl`
-    scripts=`dirname $scripts`
-    scripts="$scripts/../../scripts"
-    echo "Done!"
-fi
-
-read=$1
-k=$2
-asm1_fa=$3
-asm2_fa=$4
-name=$5
-
-if [ -z $name ]; then
-	name=$4
-	asm2_fa=""
-fi
-
-if [ -s $name ]; then
-        echo "$name already exists. Provide a different name."
-        exit -1
-fi
-
-
-## Remove this line if R is properly installed ##
-module load R					#
-#################################################
-
-asm1=`echo $asm1_fa | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
-
-echo "Generate spectra-cn.hist per assemblies"
-for asm_fa in $asm1_fa $asm2_fa	# will generate only for asm1_fa if asm2_fa is empty
-do
-	asm=`echo $asm_fa | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
-
-	# Generate meryl db per assembly
-	if [ ! -e $asm.meryl ]; then
-	    echo
-	    echo "Generate meryl db for $asm"
-	    meryl count memory=31 k=$k output ${asm}.meryl $asm_fa
-	fi
-
-	echo
-	echo "Collect read counts per asm copies"
-	hist=$name.asm.$asm.spectra-cn.hist
-	echo -e "Copies\tkmer_multiplicity\tCount" > $hist
-	echo "
-	meryl difference output read.k$k.$asm.0.meryl $read $asm.meryl"
-	meryl difference output read.k$k.$asm.0.meryl $read $asm.meryl
-	meryl histogram read.k$k.$asm.0.meryl | awk '{print "read-only\t"$0}' >> $hist
-
-	for i in $(seq 1 4)
-	do
-	    echo "
-	    meryl intersect output read.k$k.$asm.$i.meryl $read [ equal-to $i ${asm}.meryl ]"
-	    meryl intersect output read.k$k.$asm.$i.meryl $read [ equal-to $i ${asm}.meryl ]
-	    meryl histogram read.k$k.$asm.$i.meryl | awk -v cn=$i '{print cn"\t"$0}' >> $hist
-	    rm -r read.k$k.$asm.$i.meryl
-	done
-	echo "
-	meryl intersect output read.k$k.$asm.gt$i.meryl $read [ greater-than $i ${asm}.meryl ]"
-	meryl intersect output read.k$k.$asm.gt$i.meryl $read [ greater-than $i ${asm}.meryl ]
-	meryl histogram read.k$k.$asm.gt$i.meryl | awk -v cn=">$i" '{print cn"\t"$0}' >> $hist
-	rm -r read.k$k.$asm.gt$i.meryl
-
-	echo "
-	meryl difference output $asm.0.meryl ${asm}.meryl $read"
-	meryl difference output $asm.0.meryl ${asm}.meryl $read
-	meryl statistics ${asm}.0.meryl  | head -n4 | tail -n1 | awk -v asm=$asm '{print asm"\t"$1"\t"$2}' >> $name.asmonly.txt
-
-	echo "Plot $hist"
-	echo "
-	$scripts/plot/plot_spectra_cn.R -f $hist -o $name.asm.$asm"
-	$scripts/plot/plot_spectra_cn.R -f $hist -o $name.asm.$asm
-
-	ASM_ONLY=`meryl statistics ${asm}.0.meryl  | head -n4 | tail -n1 | awk '{print $2}'`
-        TOTAL=`meryl statistics ${asm}.meryl  | head -n4 | tail -n1 | awk '{print $2}'`
-        ERROR=`echo "$ASM_ONLY $TOTAL" | awk -v k=$k '{print (1-(1-$1/$2)^(1/k))}'`
-        QV=`echo "$ASM_ONLY $TOTAL" | awk -v k=$k '{print (-10*log(1-(1-$1/$2)^(1/k))/log(10))}'`
-        echo -e "$asm\t$ASM_ONLY\t$TOTAL\t$QV\t$ERROR" >> $name.qv
-done
-
-if [[ "$asm2_fa" = "" ]]; then
-	echo "No asm2_fa given. Done."
-
-	hist=$name.spectra-asm.hist
-
-	# $asm1 only
-	meryl intersect output read.k$k.$asm1.meryl $read ${asm1}.meryl
-
-	# Write output
-	echo -e "Assembly\tkmer_multiplicity\tCount" > $hist
-	meryl histogram read.k$k.$asm1.0.meryl | awk '{print "read-only\t"$0}' >> $hist
-	meryl histogram read.k$k.$asm1.meryl | awk -v hap="$asm1" '{print hap"\t"$0}' >> $hist
-
-	echo "
-	Plot $hist"
-	echo "
-	$scripts/plot/plot_spectra_asm.R -f $hist -o $name.asm"
-	$scripts/plot/plot_spectra_asm.R -f $hist -o $name.asm
-
-	echo "Clean up"
-	rm -r ${asm1}.0.meryl read.k$k.$asm1.0.meryl read.k$k.$asm1.meryl
-
-
-	exit 0
-fi
-asm2=`echo $asm2_fa | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
-rm -r read.k$k.$asm2.0.meryl
-
-echo
-echo "Generate spectra-cn.hist for combined $asm1_fa and $asm2_fa"
-echo "\"Is my diploid assembly having k-mers in expected copy numbers?\""
-hist=$name.spectra-cn.hist
-
-echo "
-Union-sum: ${asm1} + ${asm2} + shared kmer counts (asm)"
-meryl union-sum output ${asm1}_${asm2}_union.meryl ${asm1}.meryl ${asm2}.meryl
-
-echo "
-0-counts in the asm; only seen in the reads"
-meryl difference output read.k$k.0.meryl $read ${asm1}_${asm2}_union.meryl
-echo
-
-echo -e "Copies\tkmer_multiplicity\tCount" > $hist
-meryl histogram read.k$k.0.meryl | awk '{print "read-only\t"$0}' >> $hist
-for i in $(seq 1 4)
-do
-    echo "
-    meryl intersect output read.k$k.$i.meryl $read [ equal-to $i ${asm1}_${asm2}_union.meryl ]"
-    meryl intersect output read.k$k.$i.meryl $read [ equal-to $i ${asm1}_${asm2}_union.meryl ]
-    meryl histogram read.k$k.$i.meryl | awk -v cn=$i '{print cn"\t"$0}' >> $hist
-    rm -r read.k$k.$i.meryl
-done
-
-echo "
-meryl intersect output read.k$k.gt$i.meryl $read [ greater-than $i ${asm1}_${asm2}_union.meryl ]"
-meryl intersect output read.k$k.gt$i.meryl $read [ greater-than $i ${asm1}_${asm2}_union.meryl ]
-meryl histogram read.k$k.gt$i.meryl | awk -v cn=">$i" '{print cn"\t"$0}' >> $hist
-rm -r read.k$k.gt$i.meryl
-
-echo "
-Plot $name.spectra-cn.hist"
-echo "
-$scripts/plot/plot_spectra_cn.R -f $hist -o $name"
-$scripts/plot/plot_spectra_cn.R -f $hist -o $name
-
-echo "
-## Count k-mers only seen in the assemblies, not in the reads ##"
-echo "
-0-counts in the read; only seen in the assembly"
-meryl difference output ${asm1}_or_${asm2}.0.meryl ${asm1}_${asm2}_union.meryl $read
-meryl intersect output ${asm1}_and_${asm2}.0.meryl $asm1.0.meryl $asm2.0.meryl
-
-meryl statistics ${asm1}_or_${asm2}.0.meryl  | head -n4 | tail -n1 | awk '{print "both\t"$1"\t"$2}' >> $name.asmonly.txt
-meryl statistics ${asm1}_and_${asm2}.0.meryl | head -n4 | tail -n1 | awk '{print "shared\t"$1"\t"$2}' >> $name.asmonly.txt
-
-echo "
-Get QV"
-ASM_ONLY=`meryl statistics ${asm1}_or_${asm2}.0.meryl  | head -n4 | tail -n1 | awk '{print $2}'`
-TOTAL=`meryl statistics ${asm1}_${asm2}_union.meryl | head -n4 | tail -n1 | awk '{print $2}'`
-ERROR=`echo "$ASM_ONLY $TOTAL" | awk -v k=$k '{print (1-(1-$1/$2)^(1/k))}'`
-QV=`echo "$ASM_ONLY $TOTAL" | awk -v k=$k '{print (-10*log(1-(1-$1/$2)^(1/k))/log(10))}'`
-echo -e "Both\t$ASM_ONLY\t$TOTAL\t$QV\t$ERROR" >> $name.qv
-rm -r ${asm1}_and_${asm2}.0.meryl ${asm1}_or_${asm2}.0.meryl ${asm1}_${asm2}_union.meryl ${asm1}.0.meryl ${asm2}.0.meryl
-
-echo "
-## Generate spectra-asm.hist for combined $asm1_fa and $asm2_fa ##"
-echo "\"Is the assembled distinct portion bigger in one of the two assemblies?\""
-hist=$name.spectra-asm.hist
-
-# Get ${asm1} / ${asm2} / shared kmers
-meryl difference output ${asm2}_only.meryl ${asm2}.meryl ${asm1}.meryl
-meryl difference output ${asm1}_only.meryl ${asm1}.meryl ${asm2}.meryl
-meryl intersect output ${asm1}_shrd.meryl ${asm1}.meryl ${asm2}.meryl
-
-# $asm1 only
-meryl intersect output read.k$k.$asm1.meryl $read ${asm1}_only.meryl
-
-# $asm2 only
-meryl intersect output read.k$k.$asm2.meryl $read ${asm2}_only.meryl
-
-# shared ($asm1 and $asm2)
-meryl intersect output read.k$k.shrd.meryl $read ${asm1}_shrd.meryl
-
-# Write output
-echo -e "Assembly\tkmer_multiplicity\tCount" > $hist
-meryl histogram read.k$k.0.meryl | awk '{print "read-only\t"$0}' >> $hist
-meryl histogram read.k$k.$asm1.meryl | awk -v hap="$asm1-only" '{print hap"\t"$0}' >> $hist
-meryl histogram read.k$k.$asm2.meryl | awk -v hap="$asm2-only" '{print hap"\t"$0}' >> $hist
-meryl histogram read.k$k.shrd.meryl | awk -v hap="shared" '{print hap"\t"$0}' >> $hist
-
-echo "
-Plot $hist"
-echo "
-$scripts/plot/plot_spectra_asm.R -f $hist -o $name.asm"
-$scripts/plot/plot_spectra_asm.R -f $hist -o $name.asm
-
-echo "
-Clean up"
-rm -r read.k$k.0.meryl read.k$k.$asm1.meryl read.k$k.$asm2.meryl read.k$k.shrd.meryl ${asm1}_only.meryl ${asm2}_only.meryl ${asm1}_shrd.meryl
-
diff --git a/scripts/plot/plot_blob.R b/scripts/plot/plot_blob.R
deleted file mode 100755
index 932f6d5..0000000
--- a/scripts/plot/plot_blob.R
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env Rscript
-
-require("argparse")
-require("ggplot2")
-require("scales")
-
-parser <- ArgumentParser(description = "Make blob plots.")
-parser$add_argument("-f", "--file", type="character", help=".count tdf; with headers; ie. <category> <seqId> <hap1Count> <hap2Count> <seqSize> (required)", default=NULL)
-parser$add_argument("-o", "--output", type="character", default="hapmers.blob", help="output prefix [default %(default)s]")
-parser$add_argument("-x", "--xdim", type="double", default=6.5, help="width of output plot [default %(default)s]")
-parser$add_argument("-y", "--ydim", type="double", default=6, help="height of output plot [default %(default)s]")
-args <- parser$parse_args()
-
-blob_plot <- function(dat, out, w=6.5, h=6) {
-
-  dat=read.table(dat, header=TRUE)
-
-  max_total=max(max(dat[,3]), max(dat[,4])) * 1.01
-  col_lab=names(dat)[1]
-  x_lab=names(dat)[3]
-  y_lab=names(dat)[4]
-  print(x_lab)
-  print(y_lab)
-
-  ggplot(dat, aes(x=dat[,3], y=dat[,4], color=dat[,1], size=dat[,5])) +
-    geom_point(shape=16) + theme_bw() +
-    scale_color_brewer(palette = "Set1") +
-    scale_fill_brewer(palette = "Set1") +     # Set1 -> Red / Blue. Set2 -> Green / Orange.
-    scale_x_continuous(labels=comma, limits = c(0, max_total)) +
-    scale_y_continuous(labels=comma, limits = c(0, max_total)) +
-    scale_size_continuous(labels=comma, range = c(1, 10), name = "Total k-mers") +
-    theme(legend.text = element_text(size=11),
-          legend.position = c(0.83,0.70),  # Modify this if the legend is covering your favorite circle
-          legend.background = element_rect(size=0.5, linetype="solid", colour ="black"),
-          axis.title=element_text(size=14,face="bold"),
-          axis.text=element_text(size=12, face="bold")) +
-    guides( size = guide_legend(order = 1),
-            colour = guide_legend(override.aes = list(size=5), order = 2, title = col_lab)) +
-    xlab(x_lab) + ylab(y_lab)
-  
-  ggsave(file = paste(out, '.png', sep=""), height = h, width = w)
-  ggsave(file = paste(out, '.pdf', sep=""), height = 2*h, width = 2*w)
-
-}
-
-blob_plot(args$file, args$output, args$xdim, args$ydim)
-
diff --git a/scripts/plot/plot_block.sh b/scripts/plot/plot_block.sh
deleted file mode 100755
index 348f762..0000000
--- a/scripts/plot/plot_block.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/bash
-
-if [[ $# -lt 4 ]]; then
-	echo "Usage: ./plot_block.sh <in.sort.bed> <out> <num_switch> <short_range> [include_gaps]"
-	echo "	<in.sort.bed>:	generated with trio/phase_block.sh"
-	echo "	<out>:		output prefix; automatically appends given <num_switch> and <short_range>"
-	echo "	<num_switch>:	number of switches allowed in <short_range>"
-	echo "	<short_range>:	interval to be determined as short-range switch (bp)"
-	echo "	<include_gaps>:	T for including gaps. Only set for phased assemblies"
-	echo "Arang Rhie, 2020-01-07. arrhie@gmail.com"
-	exit -1
-fi
-
-bed=$1
-out=$2
-num_switch=$3
-short_range=$4
-include_gaps=$5
-
-out=$out.${num_switch}_$short_range
-
-if [ -z $scripts ]; then
-    echo "Setting \$scripts path"
-    scripts=`which meryl`
-    scripts=`dirname $scripts`
-    scripts="$scripts/../../scripts"
-    scripts=`readlink -e $scripts`
-    echo "Done!"
-fi
-
-if [ -s $out.phased_block.bed 2> /dev/null ]; then
-	rm $out.phased_block.bed
-	rm $out.switch.bed 2> /dev/null
-fi
-
-echo "
-java -jar -Xmx1g $scripts/trio/bedMerToPhaseBlock.jar $bed $out $num_switch $short_range $include_gaps"
-java -jar -Xmx1g $scripts/trio/bedMerToPhaseBlock.jar $bed $out $num_switch $short_range $include_gaps
-
-SWITCH_ERR=`awk -v swi=0 -v tot=0 '{swi+=$(NF-1); tot+=$NF} END { print swi"\t"tot"\t"((100.0*swi)/tot)"%" }' $out.phased_block.bed`
-echo "Num. switches / Total markers / Switch error rate (%): $SWITCH_ERR"
-
-echo "
-java -jar -Xmx1g $scripts/eval/bedCalcN50.jar $out.phased_block.bed | tail -n1 | awk -v out=$out -v swi=\"$SWITCH_ERR\" '{print out\"\t\"\$0\"\tswi}' - >> $out.phased_block.stats"
-java -jar -Xmx1g $scripts/eval/bedCalcN50.jar $out.phased_block.bed | tail -n1 | awk -v out=$out -v swi="$SWITCH_ERR" '{print out"\t"$0"\t"swi}' - >> $out.phased_block.stats
-
-count=$out.phased_block.counts
-
-echo -e "Block\tRange\tMat\tPat\tSize" > $count
-awk '{ swi=$(NF-1); tot=$NF; {if ($4=="mat") { mat=(tot-swi); pat=swi; } else if ($4=="pat") { mat=swi; pat=(tot-swi); }} {print $4"\t"$1"_"$2"_"$3"\t"mat"\t"pat"\t"($3-$2)}}' $out.phased_block.bed >> $count
-
-module load R
-
-echo "
-Rscript $scripts/plot/plot_blob.R -f $count -o $out.phased_block.blob"
-Rscript $scripts/plot/plot_blob.R -f $count -o $out.phased_block.blob
-
-
diff --git a/scripts/plot/plot_spectra_asm.R b/scripts/plot/plot_spectra_asm.R
deleted file mode 100755
index c0ab59c..0000000
--- a/scripts/plot/plot_spectra_asm.R
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/usr/bin/env Rscript
-
-require("argparse")
-require("ggplot2")
-require("scales")
-
-parser <- ArgumentParser(description = "Make spectra-asm plots. Line and filled pectra-asm plots will be generated.")
-parser$add_argument("-f", "--file", type="character", help=".spectra-hap.hist file (required)", default=NULL)
-parser$add_argument("-o", "--output", type="character", help="output prefix (required)")
-parser$add_argument("-x", "--xdim", type="double", default=6, help="width of plot [default %(default)s]")
-parser$add_argument("-y", "--ydim", type="double", default=3, help="height of plot [default %(default)s]")
-parser$add_argument("-m", "--xmax", type="integer", default=150, help="maximum limit for k-mer multiplicity. [default %(default)s]")
-parser$add_argument("-c", "--ymax", type="integer", default=0, help="maximum limit for Count. If 0 is given, ymax will be auto detected by max Counts ignoring read-total and read-only. [default %(default)s]")
-args <- parser$parse_args()
-
-spectra_asm_plot  <-  function(hist, name, w=6, h=3, x_max=150, y_max=0) {
-  
-  dat=read.table(hist, header = TRUE)
-
-  if (y_max==0) {
-    y_max=max(dat[dat[,1]!="read-total" & dat[,1]!="read-only",]$Count)
-    y_max=y_max*1.5
-  }
-  print(paste("y_max:", y_max, sep=" "))
-
-
-  dat[,1]=factor(dat[,1], levels=unique(dat[,1]), ordered=TRUE) # Lock in the order  
-  
-  ## Line graph
-  ggplot(data=dat, aes(x=kmer_multiplicity, y=Count, group=dat[,1], colour=dat[,1])) +
-    geom_line() +
-    theme_bw() +
-    scale_color_brewer(palette = "Set1") +
-    scale_y_continuous(labels=comma) +
-    coord_cartesian(xlim=c(0,x_max), ylim=c(0,y_max)) +
-    labs(fill="k-mer", colour="k-mer")
-  ggsave(file = paste(name, 'ln.png', sep = "."), height = h, width = w)
-  ggsave(file = paste(name, 'ln.pdf', sep = "."), height = h, width = w)
-  
-  ## Area under the curve filled
-  ggplot(data=dat, aes(x=kmer_multiplicity, y=Count)) +
-    geom_ribbon(aes(ymin=0, ymax=pmax(Count,0), fill=dat[,1], colour=dat[,1]), alpha=0.5, linetype=1) +
-    theme_bw() +
-    scale_color_brewer(palette = "Set1", direction=1) +  # , breaks=rev(levels(dat$Assembly))
-    scale_fill_brewer(palette = "Set1", direction=1) +   # , breaks=rev(levels(dat$Assembly))
-    scale_y_continuous(labels=comma) +
-    coord_cartesian(xlim=c(0,x_max), ylim=c(0,y_max)) +
-    labs(fill="k-mer", colour="k-mer")
-  ggsave(file = paste(name, 'fl.png', sep = "."), height = h, width = w)
-  ggsave(file = paste(name, 'fl.pdf', sep = "."), height = h, width = w)
-}
-
-spectra_asm_plot(args$file, args$output, args$xdim, args$ydim, args$xmax, args$ymax)
diff --git a/scripts/plot/plot_spectra_cn.R b/scripts/plot/plot_spectra_cn.R
deleted file mode 100755
index 5de5f18..0000000
--- a/scripts/plot/plot_spectra_cn.R
+++ /dev/null
@@ -1,66 +0,0 @@
-#!/usr/bin/env Rscript
-
-require("argparse")
-require("ggplot2")
-require("scales")
-
-parser <- ArgumentParser(description = "Make spectra-cn plots. Line, filled, and stacked spectra-cn plots will be generated.")
-parser$add_argument("-f", "--file", type="character", help=".spectra-cn.hist file (required)", default=NULL)
-parser$add_argument("-o", "--output", type="character", help="output prefix (required)")
-parser$add_argument("-x", "--xdim", type="double", default=6, help="width of plot [default %(default)s]")
-parser$add_argument("-y", "--ydim", type="double", default=3, help="height of plot [default %(default)s]")
-parser$add_argument("-m", "--max", type="integer", default=150, help="maximum limit for k-mer multiplicity [default %(default)s]")
-args <- parser$parse_args()
-
-spectra_cn_plot  <-  function(hist, name, w=5, h=3, x_max=150) {
-  
-  dat=read.table(hist, header=TRUE)
-  
-  y_max=max(dat[dat[,1]!="read-only",]$Count)
-  y_max=y_max*1.5
-  print(paste("y_max:", y_max, sep=" "))
-
-  if ( length(levels(dat[,1])) == 6 ) {
-    dat[,1]=factor(dat[,1], levels=levels(dat[,1])[c(6,2,3,4,5,1)])
-  } else if ( length(levels(dat[,1])) == 4 ) {
-    dat[,1]=factor(dat[,1], levels=levels(dat[,1])[c(3,1,2,4)])
-  }
-    
-  ## Line graph
-  ggplot(data=dat, aes(x=kmer_multiplicity, y=Count, group=dat[,1], colour=dat[,1])) +
-    geom_line() +
-    theme_bw() +
-    scale_color_brewer(palette = "Set1", name="k-mer") +
-    scale_y_continuous(labels=comma) +
-    coord_cartesian(xlim=c(0,x_max), ylim=c(0,y_max))
-  ggsave(file = paste(name, 'spectra-cn.ln.png', sep = "."), height = h, width = w)
-  ggsave(file = paste(name, 'spectra-cn.ln.pdf', sep = "."), height = h, width = w)
-  
-  ## Area under the curve filled
-  ggplot(data=dat, aes(x=kmer_multiplicity, y=Count)) +
-    geom_ribbon(aes(ymin=0, ymax=pmax(Count,0), fill=dat[,1], colour=dat[,1]), alpha=0.5, linetype=1) +
-    theme_bw() +
-    scale_color_brewer(palette = "Set1", direction=1, name="k-mer") +  # , breaks=rev(levels(dat$kmer))
-    scale_fill_brewer(palette = "Set1", direction=1, name="k-mer") +   # , breaks=rev(levels(dat$kmer))
-    scale_y_continuous(labels=comma) +
-    coord_cartesian(xlim=c(0,x_max), ylim=c(0,y_max))
-  
-  ggsave(file = paste(name, 'spectra-cn.fl.png', sep = "."), height = h, width = w)
-  ggsave(file = paste(name, 'spectra-cn.fl.pdf', sep = "."), height = h, width = w)
-  
-  ## Stacked
-  dat[,1]=factor(dat[,1], levels=rev(levels(dat[,1]))) #[c(4,3,2,1)])
-  ggplot(data=dat, aes(x=kmer_multiplicity, y=Count, group=dat[,1], fill=dat[,1])) +
-    geom_area(size=.5, alpha=1) +
-    theme_bw() +
-    scale_color_brewer(palette = "Set1", direction=-1, name="k-mer", breaks=rev(levels(dat[,1]))) +
-    scale_fill_brewer(palette="Set1", direction=-1, name="k-mer", breaks=rev(levels(dat[,1]))) +
-    scale_y_continuous(labels=comma) +
-    coord_cartesian(xlim=c(0,x_max), ylim=c(0,y_max)) # xlim(0, x_max) + ylim(0,y_max)
-  
-  ggsave(file = paste(name, 'spectra-cn.stacked.png', sep = "."), height = h, width = w)
-  ggsave(file = paste(name, 'spectra-cn.stacked.pdf', sep = "."), height = h, width = w)
-}
-
-spectra_cn_plot(args$file, args$output, args$xdim, args$ydim, args$max)
-
diff --git a/scripts/trio/bedMerToPhaseBlock.jar b/scripts/trio/bedMerToPhaseBlock.jar
deleted file mode 100755
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diff --git a/scripts/trio/exclude_reads.sh b/scripts/trio/exclude_reads.sh
deleted file mode 100755
index 201ec2e..0000000
--- a/scripts/trio/exclude_reads.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-
-if [[ $# -lt 4 ]]; then
-	echo "Usage: ./exclude_reads.sh <in.meryl> <R1.fastq.gz> <R2.fastq.gz> <out.prefix>"
-	echo "When a read has a k-mer in <in.meryl>, both pairs will be excluded."
-	echo -e "\t<in.meryl>   : meryl db to lookup"
-	echo -e "\t<R1.fastq.gz>: read 1 fastq file."
-	echo -e "\t<R2.fastq.gz>: read 2 fastq file."
-	echo -e "\t<out.prefix> : <out.prefix>.R1.fastq.gz and <out.prefix>.R2.fastq.gz will be generated."
-	exit -1
-fi
-
-meryl=$1
-read1=$2
-read2=$3
-out=$4
-
-echo "
-meryl-lookup -memory 2 -exclude -mers $meryl -sequence $read1 -sequence2 $read2 -r2 $out.R2.fastq.gz | pigz -c > $out.R1.fastq.gz"
-meryl-lookup -memory 2 -exclude -mers $meryl -sequence $read1 -sequence2 $read2 -r2 $out.R2.fastq.gz | pigz -c > $out.R1.fastq.gz
-
diff --git a/scripts/trio/fastaGetGaps.jar b/scripts/trio/fastaGetGaps.jar
deleted file mode 100755
index 7687cff411a277aef2ea4cffb82204af529c69b7..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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diff --git a/scripts/trio/hap_blob.sh b/scripts/trio/hap_blob.sh
deleted file mode 100755
index 023873b..0000000
--- a/scripts/trio/hap_blob.sh
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/bin/bash
-
-
-echo "Usage: ./hap_blob.sh <hap1.meryl> <hap2.meryl> <asm1.fasta> [asm2.fasta] <out>"
-
-if [[ $# -lt 4 ]]; then
-	exit -1
-fi
-
-hap1=$1
-hap2=$2
-asm1=$3
-asm2=$4
-out=$5
-
-if [[ -z $hap1 || -z $hap2 ]]; then
-	echo "Check <hap1.meryl> and <hap2.meryl>."
-	exit -1
-fi
-
-if [[ -z $asm1 ]]; then
-	echo "No .fasta file given. Exit."
-	exit -1
-fi
-
-if [[ -z $out ]]; then
-	echo "No asm2 given."
-	echo
-	asm2=""
-	out=$4
-fi
-
-if [ -z $scripts ]; then
-    echo "Setting \$scripts path"
-    scripts=`which meryl`
-    scripts=`dirname $scripts`
-    scripts="$scripts/../../scripts"
-    echo "Done!"
-fi
-
-count=$out.hapmers.count
-echo -e "Assembly\tContig\t${hap1/.meryl}\t${hap2/.meryl}\tSize" > $count
-for asm in $asm1 $asm2
-do
-	name=`echo $asm | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
-	echo "
-	Start processing $name"
-
-	for hap in $hap1 $hap2
-	do
-		hap_name=${hap/.meryl}
-		if [ -s $name.$hap_name.count ]; then
-			echo "Found $name.$hap_name.count"
-		else
-			echo -e "\n\n--- Count k-mers in $hap_name ---
-			meryl-lookup -existence -sequence $asm -mers $hap > $name.$hap_name.count"
-			meryl-lookup -existence -sequence $asm -mers $hap > $name.$hap_name.count
-		fi
-	done
-
-	awk -v asm=$name '{print asm"\t"$1"\t"$NF}' $name.${hap1/.meryl/}.count > $asm.tmp
-	awk '{print $NF"\t"$(NF-2)}' $name.${hap2/.meryl/}.count | paste $asm.tmp - >> $count
-	rm $asm.tmp
-done
-
-echo "
-Plot hap-mer blob plots"
-
-module load R
-
-echo "
-Rscript $scripts/plot/plot_blob.R -f $count -o $out.hapmers.blob"
-Rscript $scripts/plot/plot_blob.R -f $count -o $out.hapmers.blob
-
diff --git a/scripts/trio/phase_block.sh b/scripts/trio/phase_block.sh
deleted file mode 100755
index 4c37d4f..0000000
--- a/scripts/trio/phase_block.sh
+++ /dev/null
@@ -1,68 +0,0 @@
-#!/bin/bash
-
-echo "Usage: ./phase_block.sh <asm.fasta> <hap1.meryl> <hap2.meryl> <out>"
-
-if [[ $# -lt 4 ]]; then
-	exit -1
-fi
-
-scaff=$1
-scaff=${scaff/.fasta/}
-
-hap1=$2
-hap2=$3
-out=$4
-
-if [ -z $scripts ]; then
-    echo "Setting \$scripts path"
-    scripts=`which meryl`
-    scripts=`dirname $scripts`
-    scripts="$scripts/../../scripts"
-    scripts=`readlink -e $scripts`
-    echo "Done!"
-fi
-
-module load bedtools
-module load samtools
-igvtools=$tools/IGVTools/igvtools
-
-
-if [ ! -e $scaff.gaps ]; then
-	echo "
-	Get gaps"
-	java -jar -Xmx4g $scripts/trio/fastaGetGaps.jar $scaff.fasta $scaff.gaps
-fi
-awk '{print $1"\t"$2"\t"$3"\tgap"}' $scaff.gaps > $scaff.gaps.bed
-cat $scaff.gaps.bed > $scaff.bed
-
-samtools faidx $scaff.fasta
-
-if [ ! -s $out.sort.bed ]; then
-	echo "
-	Generate pat and mat marker sites bed"
-	for hap in $hap1 $hap2
-	do
-		hap=${hap/.meryl/}
-		echo "
-		-- $hap"
-		hap_short=${hap/.inherited/}
-		if [ ! -s $out.$hap.bed ]; then
-			meryl-lookup -dump -memory 4 -sequence $scaff.fasta -mers $hap.meryl | awk -v hap=$hap_short '$(NF-4)=="T" {print $1"\t"$(NF-5)"\t"($(NF-5)+21)"\t"hap}' > $out.$hap.bed
-		fi
-		cat $out.$hap.bed >> $out.bed
-
-		if [ ! -s $out.$hap.$tdf ]; then
-			$igvtools count $out.$hap.bed $out.$hap.tdf $scaff.fasta.fai
-		fi
-	done
-
-	echo "
-	Sort $out.bed"
-	bedtools sort -i $out.bed > $out.sort.bed
-fi
-
-#$scripts/plot/plot_block.sh <in.sort.bed> <out> <num_switch> <short_range> [include_gaps] 
-echo "
-$scripts/plot/plot_block.sh $out.sort.bed $out 10 20000 T"
-$scripts/plot/plot_block.sh $out.sort.bed $out 10 20000 T
-
diff --git a/scripts/trio/spectra-hap.sh b/scripts/trio/spectra-hap.sh
deleted file mode 100755
index d24491b..0000000
--- a/scripts/trio/spectra-hap.sh
+++ /dev/null
@@ -1,107 +0,0 @@
-#!/bin/bash
-
-echo "Usage: ./spectra-hap-cn.sh <reads.meryl> <hap1.meryl> <hap2.meryl> <k> <asm1.fasta> [asm2.fasta] <out-prefix>"
-if [[ $# -lt 6 ]]; then
-	echo "Not enough arguements given."
-	exit -1
-fi
-
-read=$1
-read_hap1=$2 # .meryl    Haplotype1 specific kmers with counts from reads
-read_hap2=$3 # .meryl    Haplotype2 specific kmers with counts from reads
-k=$4    # kmer
-asm1_fa=$5 # .fasta    Haplotype1 assembly
-asm2_fa=$6 # .fasta    Haplotype2 assembly
-name=$7    # output prefix
-if [ -z $name ]; then
-	name=$6
-	asm2_fa=""
-fi
-
-if [ -z $read_hap1 ]; then
-	echo "No input provided. Exit."
-	exit -1
-fi
-
-if [ -z $scripts ]; then
-    echo "Setting \$scripts path"
-    scripts=`which meryl`
-    scripts=`dirname $scripts`
-    scripts="$scripts/../../scripts"
-    echo "Done!"
-fi
-
-read=${read/.meryl/}		  # all read counts
-read_hap1=${read_hap1/.meryl/}    # pat specific mers with read counts
-read_hap2=${read_hap2/.meryl/}    # mat specific mers with read counts
-
-hap_hist=$name.hapmers.hist
-cn_hist=$name.spectra-hap-cn.hist
-
-# Get histogram from all and inherited hap-mers
-echo -e "Assembly\tkmer_multiplicity\tCount" > $hap_hist
-meryl histogram $read.meryl | awk -v asm="read-total" '{print asm"\t"$0}' >> $hap_hist
-
-for hap in $read_hap1 $read_hap2
-do
-    meryl histogram $hap.meryl | awk -v asm="${hap}" '{print asm"\t"$0}' >> $hap_hist
-done
-
-## Remove this line if R is properly installed ##
-module load R                                   #
-#################################################
-
-echo "
-$scripts/plot/plot_spectra_asm.R -f $hap_hist -o ${hap_hist/.hist/}"
-$scripts/plot/plot_spectra_asm.R -f $hap_hist -o ${hap_hist/.hist/}
-
-for asm_fa in $asm1_fa $asm2_fa
-do
-    asm=`echo $asm_fa | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
-    if ! [[ "$(ls -A $asm.meryl 2> /dev/null )" ]]; then
-        echo "Generate meryl db for $asm_fa"
-        meryl count k=$k output $asm.meryl $asm_fa
-    fi
-    
-    # For each haplotype
-    for read_hap in $read_hap1 $read_hap2
-    do
-	read_hap=${read_hap/.meryl/}
-
-	echo -e "Start processing $read_hap from $asm\n"
-
-        echo -e "Copies\tkmer_multiplicity\tCount" > $asm.$read_hap.$cn_hist
-
-	# Convert counts to read_hap counts
-	meryl intersect output $read_hap.$asm.meryl $read_hap.meryl $asm.meryl
-	#meryl statistics $read_hap.$asm.meryl | head -n3 | tail -n1 | awk -v asm=$asm -v read=$read '{print asm"\t"read"\t"$1"\t"$2}' >> hap.counts
-	#meryl statistics $read_hap.$asm.meryl | head -n4 | tail -n1 | awk -v asm=$asm -v read=$read '{print asm"\t"read"\t"$1"\t"$2}' >> hap.counts
-	#meryl histogram $read_hap.$asm.meryl  | awk -v asm=$asm '{print asm"\t"$0}' >> $read_hap.$hap_hist
-	#rm -r $read_hap.$asm.meryl
-
-	# Copy-number histogram per haplotype specific k-mers
-        meryl difference output read.$read_hap.0.meryl $read_hap.meryl $asm.meryl
-        meryl histogram read.$read_hap.0.meryl | awk -v read=$read_hap '{print read"-only\t"$0}' >> $asm.$read_hap.$cn_hist
-        rm -r read.$read_hap.0.meryl
-
-	for i in $(seq 1 4)
-	do
-	    meryl intersect output read.$read_hap.$i.meryl $read_hap.$asm.meryl [ equal-to $i ${asm}.meryl ]
-	    meryl histogram read.$read_hap.$i.meryl | awk -v cn=$i '{print cn"\t"$0}' >> $asm.$read_hap.$cn_hist
-	    rm -r read.$read_hap.$i.meryl
-	done
-
-	meryl intersect output read.$read_hap.gt$i.meryl $read_hap.$asm.meryl [ greater-than $i ${asm}.meryl ]
-	meryl histogram read.$read_hap.gt$i.meryl | awk -v cn=">$i" '{print cn"\t"$0}' >> $asm.$read_hap.$cn_hist
-	rm -r read.$read_hap.gt$i.meryl
-	rm -r $read_hap.$asm.meryl
-
-        echo "
-        $scripts/plot/plot_spectra_cn.R -f $asm.$read_hap.$cn_hist -o $name.$asm.$read_hap"
-        $scripts/plot/plot_spectra_cn.R -f $asm.$read_hap.$cn_hist -o $name.$asm.$read_hap
-
-    done
-
-done
-
-