Latest revision as of 00:13, 26 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: @@
+=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
-#Thetas,Tajima,Neutrality test needs documentation and examples files
+N0=theta/regionsize/4/u
+.0/30000000.0/4.0/u=10000
-#doMajorMinor 4 fjerner sites som ikke har major/minor som ref. total maerkeligt og fucked up
+from ms to realtime and realsize
-#user custom class missing
+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
+Theta is third value.
-#-samglfclean not documented
+N0=theta/2/u/s
-#soap usage is not documented
+from psmc time to realtime
+*g*N0*times
-#-sites does not work without all chromsomes being in the *sites file
+from psmc time to realtime
-#-sites gives wrong chromomosome in error
+N0*lambda
-#phat does not work alone (-doMaf 8)
+=Wiki doc=
+#  check userdir is writable
+# write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
+#user custom class missing
-# make haploid 1dsfs
+=Code fix/cleanup=
-# fix wiki doc with -sites should contain -rf with curs from -sites
+#if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor tsk 7april ?
-#describe -trim! does trim 3 remove the first and last 3 bases? or just 2?
+# 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 32: / 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
-# better screen output if unsorted filtering
-=Anders changes to version 583=
-)
-Default minMaf set to -1 (instead of 0)
-)
-added
-  freqs->freq = new double[pars->numSites];
-to phatLoop
-added the if part of
-if(freq->freq==NULL)
-  freq->freq = new double[pars->numSites];
-to postFreq and likeFreq funcitons
-to stop leak + be able to run phat without postFreq/likeFreq
-)
-changed doMajorMinor 2 to choose a minor allele even if no minor allele is observed (if -minMaf is chosen the site will be removed). This avoid removing side through the majorMinorMod function. The change
-else if (bases[i]>temp){
-->
-else if (bases[i]>=temp){
-in majorMinorCounts
-)
-Estimate nInd even if -minInd 0. Else the output is wrong when -minInd 0
-filter::run changed
-e.g.
-$ANG -out out -doMajorMinor 2 -doMaf 8 -bam bam.filelist -doCounts 1 -r 1:
-before
-gunzip -c out.mafs.gz | headchromo	position	major	minor	phat	nInd
-	13999919	A	T	0.000000	10
-	13999920	G	T	0.000000	10
-	13999921	G	T	0.000000	10
-	13999922	C	T	0.000000	10
-after
-chromo	position	major	minor	phat	nInd
-	13999919	A	T	0.000000	1
-	13999920	G	T	0.000000	1
-	13999921	G	T	0.000000	1
-	13999922	C	T	0.000000	1
-	13999923	A	T	0.000000	1
-(there is only information for one individual)

User:Thorfinn: Difference between revisions

Latest revision as of 00:13, 26 January 2018

Contents

ms and psmc stuff

Wiki doc

Code fix/cleanup

Addtional methods and functionality

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