Major overhaul with many minor changes

 - updated `supercluster.tsv` and `phase-blocks.tsv` outputs, both now
   include a column for SUPERCLUSTER and PHASE_BLOCK id
 - `phase-blocks.tsv` renamed PHASE column to BLOCK_STATE
 - added more warnings for potential edit distance errors
 - added optional `print` argument to `wf_ed()`
 - fixed edge case of `wf_ed()` causing an error
 - added `max_reach_size` global variable to limit supercluster size
   explosion from large INDELs; reaches now treated as if variant is
   `max_reach_size`
 - removed obsolete query and truth specific alignment parameter options
 - collapsed and re-organized command-line argument printing
 - renamed `summary.vcf` tags `PS` to `BS` and `PF` to `FE`
 - phase and flip errors are now printed per-contig
 - phase blocks are now correctly printed if there is only one
 - if there are two INSertions at the same location, one is filtered now
 - added warning for if the ratio of heterozygous variants on each
   haplotype is too far off
 - added Dockerfile

README.md

@@ -70,7 +70,7 @@ If you do already have HTSlib installed elsewhere, make sure you've added it to
 > cd vcfdist/src
 > make
 > ./vcfdist --version
-vcfdist v2.0.3
+vcfdist v2.1.0
 ```
 
 ### Option 2: Docker Image

docs/outputs.md

@@ -37,13 +37,13 @@ This file reports for each edit (where called query sequence differs from truth
 #### phase-blocks.tsv
 Reports the size, location, and composition of each phase block.
 
-| CONTIG | START | STOP | SIZE | SUPERCLUSTERS | PHASE |
+| CONTIG | PHASE_BLOCK | START | STOP | SIZE | SUPERCLUSTERS | BLOCK_STATE |
 |-|-|-|-|-|-|
 
 #### superclusters.tsv
 Reports the size, location, and composition of each supercluster.
 
-| CONTIG | START | STOP | SIZE | QUERY1_VARS | QUERY2_VARS | TRUTH1_VARS | TRUTH2_VARS | ORIG_ED | SWAP_ED | PHASE | PHASE_BLOCK |
+| CONTIG | SUPERCLUSTER | START | STOP | SIZE | QUERY1_VARS | QUERY2_VARS | TRUTH1_VARS | TRUTH2_VARS | ORIG_ED | SWAP_ED | PHASE | PHASE_BLOCK |
 |-|-|-|-|-|-|-|-|-|-|-|-|
 
 #### query.tsv, truth.tsv
@@ -89,7 +89,8 @@ Output query and truth VCFs, standardized by vcfdist (at point C).
 | (QUERY/TRUTH)(1/2)_VARS | integer | Total variants on a particular haplotype within this region. |
 | (ORIG/SWAP)_ED | integer | Total edit distance (minimum) of supercluster for both possible phasings. |
 | PHASE | char | Character representing phasing. (=/X/?) for same, swap, unknown |
-| PHASE_BLOCK | integer | 0-based index of current phase block. |
+| PHASE_BLOCK | integer | 0-based index of current phase block within contig. |
+| BLOCK_STATE | integer | Current phase state for truth to query haplotype mapping (0 = T1Q1:T2Q2, 1 = T1Q2:Q2T1). |
 | POS | integer | 0-based index of position within contig. |
 | REF/ALT | string | String of reference/alternate sequence at this position. |
 | CREDIT | float | Fraction of partial credit this variant received. |

docs/update.md

@@ -0,0 +1,5 @@
+1. Update `vcfdist` version in `globals.h`
+2. Replace `vcfdist --help` text in `src/README.md`
+3. Update `vcfdist` version in `README.md`
+4. Build and deploy new Docker image
+5. Make new release on Github

src/Dockerfile

@@ -0,0 +1,37 @@
+FROM ubuntu:20.04
+
+# set environment variables
+ENV LANG=C.UTF-8 \
+    LC_ALL=C.UTF-8 \
+    PATH=/opt/bin/vcfdist/src:$PATH \
+    DEBIAN_FRONTEND=noninteractive \
+    LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+
+# install packages
+RUN apt-get update --fix-missing && \
+    yes | apt-get upgrade && \
+    apt-get install -y \
+    git \
+    make \
+    g++ \
+    curl \
+    wget \
+    zlib1g-dev \
+    libbz2-dev \
+    liblzma-dev
+
+# set up HTSlib
+RUN wget https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2 && \
+    tar -xvf htslib-1.17.tar.bz2
+WORKDIR ./htslib-1.17
+RUN ./configure --prefix=/usr/local && \
+    make && \
+    make install
+
+# clone repo
+WORKDIR /opt/bin
+RUN git clone https://github.com/TimD1/vcfdist
+
+# setup virtual environment
+WORKDIR /opt/bin/vcfdist/src
+RUN make

src/README.md

@@ -8,68 +8,56 @@ Required:
   <STRING>	ref.fasta	FASTA file containing draft reference sequence 
 
 Options:
+
+  Inputs/Outputs:
   -b, --bed <STRING>
       BED file containing regions to evaluate
-
   -p, --prefix <STRING> [./]
       prefix for output files (directory needs a trailing slash)
-
   -v, --verbosity <INTEGER> [1]
       printing verbosity (0: succinct, 1: default, 2:verbose)
 
+  Variant Filtering:
+  -s, --smallest-variant <INTEGER> [1]
+      minimum variant size, smaller variants ignored (SNPs are size 1)
+  -l, --largest-variant <INTEGER> [5000]
+      maximum variant size, larger variants ignored
+  --min-qual <INTEGER> [0]
+      minimum variant quality, lower qualities ignored
+  --max-qual <INTEGER> [60]
+      maximum variant quality, higher qualities kept but thresholded
+
+  ReAlignment:
   -r, --realign-only
       standardize truth and query variant representations, then exit
-
   -q, --keep-query
       do not realign query variants, keep original representation
-
   -t, --keep-truth
       do not realign truth variants, keep original representation
-
   -x, --mismatch-penalty <INTEGER> [3]
       Smith-Waterman mismatch (substitution) penalty
-
   -o, --gap-open-penalty <INTEGER> [2]
       Smith-Waterman gap opening penalty
-
   -e, --gap-extend-penalty <INTEGER> [1]
       Smith-Waterman gap extension penalty
 
-  --min-qual <INTEGER> [0]
-      minimum variant quality, lower qualities ignored
-
-  --max-qual <INTEGER> [60]
-      maximum variant quality, higher qualities kept but thresholded
-
-  -s, --smallest-variant <INTEGER> [1]
-      minimum variant size, smaller variants ignored (SNPs are size 1)
-
-  -l, --largest-variant <INTEGER> [5000]
-      maximum variant size, larger variants ignored
-
-  -i, --max-iterations <INTEGER> [4]
-      maximum iterations for expanding/merging clusters
-
-  -g, --supercluster-gap <INTEGER> [50]
-      minimum base gap between independent superclusters
+  Clustering:
+  --simple-cluster
+      instead of biWFA-based clustering, use gap-based clustering 
 
+  Utilization:
   --max-threads <INTEGER> [64]
-      maximum threads to use for precision/recall alignment
-      (haps*contigs used for wavefront clustering)
-
+      maximum threads to use for clustering and precision/recall alignment
   --max-ram <FLOAT> [64.000GB]
-      maximum RAM to use for precision/recall alignment
-      (work in-progress, more may be used in other steps)
+      (approximate) maximum RAM to use for precision/recall alignment
 
+  Miscellaneous:
   -h, --help
       show this help message
-
   -a, --advanced
-      show advanced options
-
+      show advanced options, not recommended for most users
   -c, --citation
-      please cite vcfdist if used in your analyses
-
+      please cite vcfdist if used in your analyses: thanks!
   -v, --version
-      print vcfdist version (v2.0.3)
+      print vcfdist version (v2.1.0)
 ```