Latest revision as of 23:13, 25 January 2018

ms and psmc stuff

./msHOT-lite 2 20 -t 30000 -r 6000 30000000 -eN 0.01 0.1 -eN 0.06 1 -eN 0.2 0.5 -eN 1 1 -eN 2 2 -l

N0=theta/regionsize/4/u

30000.0/30000000.0/4.0/u=10000

from ms to realtime and realsize

tk are times from ms e.g. 0.01,0.06,0.2,1,2

alpha are sizes from ms e.g. 0.1,1,0.5,1,2

truetimes in years

4*g*N0*tk

from ms to real populationsize

alpha*N0

from psmc to realtime and realsize:

PA 4+25*2+4+6 0.026254885 0.003600825 21.895293401 5.782425186 2.106578468 0.452471596 0.479814497 0.401498376 0.367130222 0.302637758 0.336141050 0.585819704 1.405835053 2.909550136 4.044915857 4.137850214 3.776532973 3.123633638 2.466466904 2.013826351 1.792827385 1.762345431 1.839956170 1.916823191 1.921452795 1.902858530 2.051184729 2.597031978 3.508703366 4.125487051 6.375234256

Theta is third value.

N0=theta/2/u/s

from psmc time to realtime

2*g*N0*times

from psmc time to realtime

N0*lambda

Wiki doc

check userdir is writable
write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
user custom class missing

Code fix/cleanup

if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor tsk 7april ?
don't quit program if a chr is not included in the -sites file
check all getoptions stderr output.
from morten shitoutput

h1 h2 h3 = 7 10 5  has less than 3 blocks. skipping
h1 h2 h3 = 8 10 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 11 5  has less than 3 blocks. skipping
h1 h2 h3 = 7 12 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 12 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 13 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 15 5  has less than 3 blocks. skipping
h1 h2 h3 = 7 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 8 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
h1…

Addtional methods and functionality

make haploid 1dsfs
simplefy filereading. from glf files
fix -doFasta for single chromosomes.

@@ Line 1: / Line 1: @@
-#doMajorMinor 4 fjerner sites som ikke har major/minor som ref. total maerkeligt og fucked up
+=ms and psmc stuff=
-#user custom class missing
+./msHOT-lite 2 20 -t 30000 -r 6000 30000000 -eN 0.01 0.1 -eN 0.06 1 -eN 0.2 0.5 -eN 1 1 -eN 2 2 -l
+N0=theta/regionsize/4/u
+.0/30000000.0/4.0/u=10000
+from ms to realtime and realsize
+tk are times from ms e.g. 0.01,0.06,0.2,1,2
+alpha are sizes from ms e.g. 0.1,1,0.5,1,2
+truetimes in years
+*g*N0*tk
+from ms to real populationsize
+alpha*N0
+from psmc to realtime and realsize:
+PA	4+25*2+4+6 0.026254885 0.003600825 21.895293401 5.782425186 2.106578468 0.452471596 0.479814497 0.401498376 0.367130222 0.302637758 0.336141050 0.585819704 1.405835053 2.909550136 4.044915857 4.137850214 3.776532973 3.123633638 2.466466904 2.013826351 1.792827385 1.762345431 1.839956170 1.916823191 1.921452795 1.902858530 2.051184729 2.597031978 3.508703366 4.125487051 6.375234256
-#-samglfclean not documented
+Theta is third value.
-#soap usage is not documented
+N0=theta/2/u/s
+from psmc time to realtime
-#-sites does not work without all chromsomes being in the *sites file
+*g*N0*times
-#-sites gives wrong chromomosome in error
+from psmc time to realtime
-#phat does not work alone (-doMaf 8)
+N0*lambda
-# make haploid 1dsfs
+=Wiki doc=
-# fix wiki doc with -sites should contain -rf with curs from -sites
+#  check userdir is writable
-#describe -trim! does trim 3 remove the first and last 3 bases? or just 2?
+# write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
+#user custom class missing
+=Code fix/cleanup=
+#if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor tsk 7april ?
+# don't quit program if a chr is not included in the -sites file
+#check all getoptions stderr output.
 # from morten shitoutput
+<pre>
 h1 h2 h3 = 7 10 5  has less than 3 blocks. skipping
 h1 h2 h3 = 8 10 5  has less than 3 blocks. skipping
@@ Line 28: / Line 58: @@
 h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
 h1…
+</pre>
-# fix -doFasta for single chromosomes. put gzwrite && bufstr.l =0 whenever we change cur
+=Addtional methods and functionality=
+# make haploid 1dsfs
-#-doMaf 4 is not working if post is not external
-#Regarding an open issue of printing %e instead o numbers, using the bombyx/lyca dataset:
-#fix   }else{
-    fprintf(stderr,"./a.out [make_bed|do_stat|validate_bed|print]\n");
-  }  in thetaStat
 # simplefy filereading. from glf files
+# fix -doFasta for single chromosomes.
-# check 1offseted in -sites file
-# add more info to -sites file output

User:Thorfinn: Difference between revisions

Latest revision as of 23:13, 25 January 2018

Contents

ms and psmc stuff

Wiki doc

Code fix/cleanup

Addtional methods and functionality

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