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.

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

Navigation menu

@@ Line 1: / Line 1: @@
-Thorfinns angsd todolist
+=ms and psmc stuff=
--1) check that close gzclose on a null pointer
+./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
-) set -outfiles=NULL in setargsstruct
+N0=theta/regionsize/4/u
-) fix return value
+.0/30000000.0/4.0/u=10000
-) write error estimation on wiki, need more info
+from ms to realtime and realsize
-. -filter to site
+tk are times from ms e.g. 0.01,0.06,0.2,1,2
-. add single pars
+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
+Theta is third value.
+N0=theta/2/u/s
+from psmc time to realtime
+*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
 <pre>
-	-> angsd version: 0.567	 build(Dec  7 2013 18:15:43)
+h1 h2 h3 = 7 10 5  has less than 3 blocks. skipping
-	-> No '-out' argument given, output files will be called 'angsdput'
+h1 h2 h3 = 8 10 5  has less than 3 blocks. skipping
-	-> Filterfile: filt supplied will generate binary representations...
+h1 h2 h3 = 10 11 5  has less than 3 blocks. skipping
-	-> Parsing chr:'1'
+h1 h2 h3 = 7 12 5  has less than 3 blocks. skipping
-	-> Parsing chr:'2'
+h1 h2 h3 = 10 12 5  has less than 3 blocks. skipping
-	-> Parsing chr:'3'
+h1 h2 h3 = 10 13 5  has less than 3 blocks. skipping
-	-> Parsing chr:'4'
+h1 h2 h3 = 10 15 5  has less than 3 blocks. skipping
-	-> Parsing chr:'5'
+h1 h2 h3 = 7 10 6  has less than 3 blocks. skipping
-	-> Parsing chr:'6'
+h1 h2 h3 = 8 10 6  has less than 3 blocks. skipping
-	-> Parsing chr:'7'
+h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
-	-> Parsing chr:'8'
+h1…
-	-> Parsing chr:'9'
-	-> Parsing chr:'10'
-	-> Parsing chr:'11'
-	-> Parsing chr:'12'
-	-> Parsing chr:'13'
-	-> Parsing chr:'14'
-	-> Parsing chr:'15'
-	-> Parsing chr:'16'
-	-> Parsing chr:'17'
-	-> Parsing chr:'18'
-	-> Parsing chr:'19'
-	-> Parsing chr:'20'
-	-> Parsing chr:'21'
-	-> Parsing chr:'22'
-	-> Parsing chr:'X'
-	-> Filtering complete: Observed: 23 different chromosomes from file:filt
-	-> [analysisKeepList.cpp] Reading binary representation:filt
-	-> [analysisKeepList.cpp] nChr: 23 loaded from binary filter file
-Filterfile contains major/minor information
-	-> [analysisKeepList.cpp] -filter is still beta, use at own risk...
-Error: For sequence data (bam,SOAP) likehoods (-GL) must be specified for frequency estimation
-thorfinn@pontus:~/gc_angsd$ ./angsd0.567/angsd -filter filt -bam list -doMajorMinor 3 -doMaf 2 -GL 1
-DEV VERSION might not work thorfinn feb 1 2013 sizeof(funkypars):128
-Command:
-./angsd0.567/angsd -filter filt -bam list -doMajorMinor 3 -doMaf 2 -GL 1
-	-> angsd version: 0.567	 build(Dec  7 2013 18:15:43)
-	-> No '-out' argument given, output files will be called 'angsdput'
-	-> [analysisKeepList.cpp] Reading binary representation:filt
-	-> [analysisKeepList.cpp] nChr: 23 loaded from binary filter file
-Filterfile contains major/minor information
 </pre>
+=Addtional methods and functionality=
+# make haploid 1dsfs
+# simplefy filereading. from glf files
+# fix -doFasta for single chromosomes.