mod README

ivazquez · Apr 4, 2014 · 4bfa2eb · 4bfa2eb
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diff --git a/changelog.md b/changelog.md
@@ -1,5 +1,13 @@
 # changelog for cloneHD/filterHD
 
+## v1.17.3 / to come
+
+*  new program `pre-filter`
+*  `--snv-pen` to `--snv-pen-high` and `--snv-pen-mult`
+*  `--baf-pen` to `--baf-pen-compl`
+*  `--cna-pen` to `--cna-pen-zero`, `--cna-pen-diff` and `cna-pen-norm`
+*  split README
+
 ## v1.17.2 / 27.03.2014
 
 *  new output: posterior per subclone, goodness of fit (GOF) per

diff --git a/docs/README-pre-filter.md b/docs/README-pre-filter.md
@@ -16,11 +16,11 @@ The program `pre-filter` can be used to remove loci based on the observed read d
 
      The windowed tracks are used for pre-filtering. They are printed for all loci to a file named `pre.track.txt`. Use this to inspect and tune the pre-filter thresholds.
 
-*    `pick-from [file]`  Pre-filter data in this file by picking loci present in `match-to`. 
+*    `--pick-from [file]`  Pre-filter data in this file by picking loci present in `match-to`. 
 
      Only loci are selected which fall into a bin also present in `match-to`. If bins in `match-to` are in kb (1000, 2000 etc., i.e. 1-1000, 1001-2000 etc.) then loci in `pick-from` are rounded to the next 1000 above.
 
-*    `match-to [file]`  Use this file as reference to pick loci in `pick-from`. 
+*    `--match-to [file]`  Use this file as reference to pick loci in `pick-from`. 
 
      Loci in this file are assumed to be equidistant (e.g. per 1 kb, not all bins need be present). The bin width is decided automatically by majority.