Normalize snarls

.gitmodules

@@ -128,3 +128,6 @@
 [submodule "deps/atomic_queue"]
 	path = deps/atomic_queue
 	url = https://github.com/max0x7ba/atomic_queue.git
+[submodule "deps/seqan"]
+	path = deps/seqan
+	url = https://github.com/seqan/seqan.git

robin_bash/debug_normalize_snarl.sh

@@ -0,0 +1,142 @@
+#!/bin/bash
+
+export VG_FULL_TRACEBACK=1
+set -e
+
+echo compiling!
+. ./source_me.sh && make -j 8
+echo running!
+
+###After Normalization
+dir=/home/robin/paten_lab/vg/test/robin_tests/chr21
+# base=hgsvc_construct.chr21.robin_made
+base=hgsvc_construct.chr21.robin_made.normalized
+haps=HGSVC.haps.vcf.gz
+threads=16
+# meta=200bp.60000num
+reads=hgsvc_construct.chr21.robin_made.normalized.read_sim.200bp.60000num.txt
+# reads=hgsvc_construct.chr21.robin_made.normalized.read_sim.400bp.5000num.txt
+
+vg map -t $threads -d $dir/$base -x $dir/$base.xg -T $dir/$reads >$dir/$base.alignment.gam
+#  vg view -a $dir/$base.alignment.gam -j >$dir/$base.alignment.$meta.json
+
+echo finished mapping.
+
+#jq arbitrary queries for gam files (vg view is easier, more weighty), vg gamcompare with an empty file lets you look at full gam.
+
+###Before Normalization (orignally used in sh file on courtyard - see reconstruct_jmonlong_chr21):
+# in_dir=/public/groups/cgl/graph-genomes/jmonlong/hgsvc/haps
+# ref=hg38.fa
+# in_dir=/home/robin/paten_lab/vg/test/robin_tests/chr21
+# vars=HGSVC.haps.vcf.gz
+# base=hgsvc_construct.chr21.robin_made
+# base_out=hgsvc_construct.chr21.robin_made.test_out
+# chrom=chr21
+# threads=8
+
+#make graph
+#vg construct -r $in_dir/$ref -v $in_dir/$vars -R $chrom -C -m 32 -a -f > $base.vg
+
+#index graph. Note: currently doesn't make .gcsa for some reason.
+# vg index -t $threads -x $in_dir/$base_out.xg -G $in_dir/$base_out.gbwt -v $in_dir/$vars -g $in_dir/$base_out.gcsa $in_dir/$base.vg
+# vg index -G hgsvc_construct.chr21.robin_made.normalized.gbwt -g hgsvc_construct.chr21.robin_made.normalized.gcsa -v HGSVC.haps.vcf.gz hgsvc_construct.chr21.robin_made.normalized.vg 
+
+#make snarls.
+# vg snarls -v $in_dir/$vars $base.vg > $base.snarls.pb
+
+# chunk graph?
+# vg chunk -x hgsvc_construct.chr21.robin_made.normalized.xg -G hgsvc_construct.chr21.robin_made.normalized.gbwt -r 0:16608 >chunk_normalized_0_to_16608.vg
+
+
+
+###Before and During Normalization
+##running normalize_snarls on a full chromosome - local machine.
+# TEST_DIR=test/robin_tests/full_chr10
+# FILE_NAME=hgsvc_chr10_construct
+# FILE_NAME_OUT=junk
+# FILE_NAME_OUT=chr10_no_gbwt_handles_at_25128
+# FILE_NAME_OUT=hgsvc_chr10_construct_normalized_no_max_size
+
+# TEST_DIR=test/robin_tests/chr21
+# FILE_NAME=hgsvc_construct.chr21.robin_made.normalized
+# FILE_NAME_OUT=hgsvc_construct.chr21.robin_made.normalized
+# FILE_NAME_OUT=hgsvc_construct.chr21.robin_made.normalized.subgraph.301929.exp_context
+
+## running full chr21:
+# vg normalize -e -g $TEST_DIR/$FILE_NAME.gbwt -s $TEST_DIR/$FILE_NAME.snarls.pb $TEST_DIR/$FILE_NAME.hg >$TEST_DIR/$FILE_NAME_OUT.hg
+
+## running subset of chr21
+# vg find -x $TEST_DIR/$FILE_NAME.xg -n 301929 -c 100 >$FILE_NAME_OUT.vg
+# ./bin/vg view -dpn $FILE_NAME_OUT.vg| \
+# dot -Tsvg -o $FILE_NAME_OUT.svg
+# chromium-browser $FILE_NAME_OUT.svg
+
+
+# vg view -dpn $FILE_NAME_OUT.vg| \
+# dot -Tsvg -o $FILE_NAME_OUT.svg
+# chromium-browser $FILE_NAME_OUT.svg
+
+## for extracting a prenormalized subgraph for looking at chr10
+
+# TEST_DIR=test/robin_tests/chr21
+# FILE_NAME=hgsvc_construct.chr21.robin_made
+# FILE_NAME_OUT=hgsvc_construct.chr21.robin_made.subgraph.301929.exp_context
+
+# vg find -x $TEST_DIR/$FILE_NAME.xg -n 301929 -c 100 >$FILE_NAME_OUT.vg
+# ./bin/vg view -dpn $FILE_NAME_OUT.vg| \
+# dot -Tsvg -o $FILE_NAME_OUT.svg
+# chromium-browser $FILE_NAME_OUT.svg
+
+
+##running full chr10
+# echo "running normalize (w/ evaluation)"
+# valgrind --leak-check=full vg normalize -e -g $TEST_DIR/$FILE_NAME.gbwt -s $TEST_DIR/$FILE_NAME.snarls $TEST_DIR/$FILE_NAME.hg >$TEST_DIR/$FILE_NAME_OUT.hg
+# vg normalize -e -g $TEST_DIR/$FILE_NAME.gbwt -s $TEST_DIR/$FILE_NAME.snarls.pb $TEST_DIR/$FILE_NAME.hg >$TEST_DIR/$FILE_NAME_OUT.hg
+
+
+# ##running full chr10 with no max size.
+# echo "running normalize (w/ evaluation)"
+# vg normalize -e -m 0 -g $TEST_DIR/$FILE_NAME.gbwt -s $TEST_DIR/$FILE_NAME.snarls $TEST_DIR/$FILE_NAME.hg >$TEST_DIR/$FILE_NAME_OUT.hg
+
+
+## for printing out the normalized subsnarl:
+# vg normalize -g $TEST_DIR/$FILE_NAME.gbwt -s $TEST_DIR/$FILE_NAME.snarls $TEST_DIR/$FILE_NAME.hg >graph_out.vg
+# ./bin/vg view -dpn graph_out.vg| \
+# dot -Tsvg -o graph_out.svg
+# chromium-browser graph_out.svg
+
+## for extracting a prenormalized subgraph for looking at chr10
+# vg find -x $TEST_DIR/$FILE_NAME.xg -n 25128 -c 25 >$FILE_NAME_OUT.vg
+# ./bin/vg view -dpn $FILE_NAME_OUT.vg| \disambiguating snarl #85 source: 23053 sink: 23075
+# dot -Tsvg -o $FILE_NAME_OUT.svg
+# chromium-browser $FILE_NAME_OUT.svg
+
+## looking at an old example
+# TEST_DIR=test/robin_tests/robin_haplotypes/complex
+# FILE_NAME=chr10_subgraph_0_new
+# FILE_NAME_OUT=chr10_subgraph_0_new_normalized_200_max_thread_size
+# # vg index -G $TEST_DIR/$FILE_NAME.gbwt -v $TEST_DIR/../../HGSVC.haps.chr10.vcf.gz $TEST_DIR/$FILE_NAME.vg
+# # vg convert -v $TEST_DIR/$FILE_NAME.vg -A >$TEST_DIR/$FILE_NAME.hg
+# vg normalize -e -g $TEST_DIR/$FILE_NAME.gbwt -s $TEST_DIR/$FILE_NAME.snarls $TEST_DIR/$FILE_NAME.hg >$TEST_DIR/$FILE_NAME_OUT.hg
+# vg convert -a $TEST_DIR/$FILE_NAME_OUT.hg -V >$TEST_DIR/$FILE_NAME_OUT.vg
+# vg mod -g 609548 -x 65 $TEST_DIR/$FILE_NAME_OUT.vg | vg view -dpn - | dot -Tsvg -o $TEST_DIR_OUT/$FILE_NAME_OUT.svg
+# chromium-browser $TEST_DIR_OUT/$FILE_NAME_OUT.svg
+
+
+
+
+### After Normalization:
+## for making a snarls file:
+# vg convert -a $TEST_DIR/$FILE_NAME_OUT.hg -V >$TEST_DIR/$FILE_NAME_OUT.vg
+# echo "hg converted to vg"
+# vg snarls $TEST_DIR/$FILE_NAME_OUT.vg >$TEST_DIR/$FILE_NAME_OUT.snarls 
+# echo ".snarls made"
+
+## for evaluating normalized graph:
+# echo "getting vg stats:"
+# vg stats -z -l $TEST_DIR/$FILE_NAME_OUT.vg
+
+## creating a new gbwt graph from the outgraph:
+# vg index -G $TEST_DIR/$FILE_NAME_OUT.gbwt -v $TEST_DIR/../HGSVC.haps.chr10.vcf.gz $TEST_DIR/$FILE_NAME_OUT.vg
+# echo "gbwt made"
+