Addressing #63

Also removing notes from collapse.py that have been placed on wiki

README.md

@@ -36,7 +36,7 @@ Each sub-command contains help documentation. Start with `truvari -h` to see ava
 
 The current most common Truvari use case is for structural variation benchmarking:
 ```
-  truvari bench -b base.vcf.gz -c comp.vcf.gz -r reference.fasta -o output_dir/
+  truvari bench -b base.vcf.gz -c comp.vcf.gz -f reference.fasta -o output_dir/
 ```
 ## Truvari Commands
 

dist_cmds.sh

@@ -1,4 +1,4 @@
 python setup.py sdist bdist_wheel
-#twine upload -r pypi dist/*
+twine upload -r pypi dist/*
 python3 -m pip install dist/*tar.gz
 

truvari/collapse.py

@@ -3,64 +3,6 @@
 
 Will collapse all variants within sizemin/max that match over thresholds
 All variants outside size boundaries will be placed into the output
-
-When collapsing, the first variant from a matching set of variants will 
-be written to the output while the others will be placed in collapsed output.
-
-Samples with no genotype information in the first variant will be filled by the first
-collapsed variant containing genotype information.
-
-ToDo:
-When using --hap, we assume phased variants from a single individual. Only the
-single best non-exact matching call from the other haplotype will be collapsed,
-and the consolidated genotype will become 1/1
-
-For example, if we collapse anything at the same position:
-
-    chr1 1 .. GT 0|1
-    chr1 1 .. GT 1|0
-    chr1 2 .. GT 1|0
-
-will become:
-    chr1 1 .. GT 1/1
-    chr1 2 .. GT 1|0
-
-When using --chain mode, instead of collapsing all variants matching the first variant
-together, we'll collapse all variants in a matching set together. 
-For example, if we have
-
-    chr1 5 ..
-    chr1 6 ..
-    chr1 7 ..
-
-When we collapse anything within 1bp of each other, without --chain, we output:
-
-    chr1 5 ..
-    chr1 7 ..
-
-With --chain, we would collapse `chr1 7` as well, producing
-
-    chr1 5 ..
-
-# Just turn this on by default... damn..
-When using --detail, we'll record detailed matching information into the 
-collapsed-output VCF entrie's infor fields (e.g. PctSim)
-
-
---null-consolidate is for special fields that should be consolidated from the FORMAT, for example,
-imagine there is a field (FL) that may be null in some entries for a sample, but we want to preserve
-the non-nulls in our kept entry:
-
-    chr1 5 .. GT:GQ:FL 0/1:32:.
-    chr1 7 .. GT:GQ:FL 0/0:.:FLAG
-
-Without `--null-consolidate FL`, that FLAG will be lost because the call is present in the @5 call (0/1),
-so no conslidation of the collapsed entry's SAMPLE information is pulled. But with `--null-consolidate FL`,
-even though there is no consolidation triggered by the GT, we'll still preserve the FL:
-    
-    chr1 5 .. GT:GQ:FL 0/1:32:FLAG
-
-This only works with Number=1/Number=0 FORMAT fields currently
 """
 # pylint: disable=too-many-statements, no-member
 import os