patch v1.17.8

README.md

@@ -108,3 +108,10 @@ prediction (red).
    of the bias field might not be very useful, especially in segmenting the tumor data.
    Use rather, if available, the jumps seen in the BAF data for both CNA and BAF data
    (give the BAF jumps file to both `--cna-jumps` and `--baf-jumps`).
+
+#How to cite
+
+The cloneHD and filterHD software is free under the GNU General Public License v3.
+If you use this software in your work, please cite the accompanying publication:
+
+Andrej Fischer, Ignacio Vazquez-Garcia, Christopher J.R. Illingworth and Ville Mustonen. High-definition reconstruction of subclonal composition in cancer. Cell Reports (2014), http://dx.doi.org/ 10.1016/j.celrep.2014.04.055

TODO.md

@@ -6,8 +6,6 @@
 
 ## cloneHD
 
-*  with `--purity` and `--clones` (mass only), `--nmax` is ignored
-*  if using BAF-jumps for CNA: mapping to be checked
 *  print full if `--*jump` is (also) given, only events if `--*jumps`
 *  check memory leaks
 
@@ -17,9 +15,9 @@
 
 *  filter loci incompatible with emission model via 2-state HMM
 *  do Baum-Welch
-*  `--filter-shortSeg [int]` via posterior jump-prob (not via pmean)!
+*  `--filter-shortSeg [int]` via posterior jump-prob (not via pmean)
 *  Use diffusion constant that scales with size in mode 3/4.
-*  Implement jump subtraction via dynamic programming.
+*  Implement jump subtraction
 
 ## cloneHD
 

changelog.md

@@ -1,16 +1,17 @@
 # changelog for cloneHD/filterHD
 
-## to come
+## v1.17.8 / 29.05.2014
 
 *  added checks whether files are open for writing
 *  changed to new defaults: `--(cna/baf/snv)-rnd [double:1.0e-6]` (nan)
-*  allowed `--cna-jump -1` and `--baf-jump -1` (subject to testing)
+*  allowed `--cna-jump -1` and `--baf-jump -1` (no jumps)
 *  `--cna-jumps [baf-jumps-file]` and vice versa enabled (useful for exome data)
-*  jumps read with new function match_jumps() (not get_track()).
+*  jumps read and integrated with new function match_jumps() (not get_track()).
+* fixed bug when chromosomes have no non-zero observations.
 
 ## v1.17.7 / 25.04.2014
 
-*  fixed range error in `pre-filter` in pick-from/match-to mode
+*  fixed range error in `pre-filter` in pick-from/match-to mode.
 
 ## v1.17.6 / 24.04.2014
 

docs/README-pre-filter.md

@@ -2,6 +2,11 @@
 
 The program `pre-filter` can be used to remove loci based on the observed read depth. It includes two heuristic filtering methods: loci are removed based on (i) their local variability and (ii) their being an outlier (see below). 
 
+![pref](/images/prefilter-1.png "Pre-filtering of read depth via matched normal.")
+
+The effect of `pre-filter` on read depth data: (A) Centromeric regions of real chromosomes often show huge large scale variability in their read depth. But there are also many small regions with very low read depth throughout. (B) After pre-filtering, the problematic regions are masked out. (C) Removing the same regions in the tumor data improves quality visibly while retaining biologically relevant features.
+
+
 ## Typical usage options
 
 *  `--data [file]`  Input data to be pre-filtered.