User:Thorfinn

Wiki doc

1. write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
2. user custom class missing

Code fix/cleanup

1. check that -doCounts imprinting with %u

./angsd -i /home/software/angsd/test/smallBam/smallNA06985.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam -r 1: -doHetPlas 1 -out temp -nThreads 22 -minQ 20 -minMapQ 30 -doCounts 1 -dumpCounts 3 -setMinDepth 10 
	-> angsd version: 0.591	 build(Apr  2 2014 11:51:03)
==9935== Invalid read of size 4
==9935==    at 0x42C635: initializeBufReaders2(std::vector<char*, std::allocator<char*> > const&) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x42CBC3: bammer_main(argStruct*) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x453D6F: multiReader::fetch() (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x4041E7: main (in /home/software/angsd/angsd0.591/angsd)
==9935==  Address 0xabd3260 is 96 bytes inside a block of size 98 alloc'd
==9935==    at 0x98E52DB: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9935==    by 0xA7CC8C1: strdup (strdup.c:42)
==9935==    by 0x42C618: initializeBufReaders2(std::vector<char*, std::allocator<char*> > const&) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x42CBC3: bammer_main(argStruct*) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x453D6F: multiReader::fetch() (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x4041E7: main (in /home/software/angsd/angsd0.591/angsd)
==9935== 
	-> Parsing 1 number of samples 
==9935== Thread 3:
==9935== Conditional jump or move depends on uninitialised value(s)
==9935==    at 0x44478A: hetplas::doNew(funkyPars*) (hetplas.cpp:189)
==9935==    by 0x4448C1: hetplas::run(funkyPars*) (hetplas.cpp:207)
==9935==    by 0x457C59: interface(funkyPars*) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x457C78: slave(void*) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x9D0FF6D: start_thread (pthread_create.c:311)
==9935==    by 0xA83D9CC: clone (clone.S:113)
==9935== 
==9935== Conditional jump or move depends on uninitialised value(s)
==9935==    at 0x98E7012: operator delete[](void*) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9935==    by 0x4447AA: hetplas::doNew(funkyPars*) (hetplas.cpp:189)
==9935==    by 0x4448C1: hetplas::run(funkyPars*) (hetplas.cpp:207)
==9935==    by 0x457C59: interface(funkyPars*) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x457C78: slave(void*) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x9D0FF6D: start_thread (pthread_create.c:311)
==9935==    by 0xA83D9CC: clone (clone.S:113)
==9935== 
==9935== Invalid free() / delete / delete[] / realloc()
==9935==    at 0x98E705C: operator delete[](void*) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9935==    by 0x4447AA: hetplas::doNew(funkyPars*) (hetplas.cpp:189)
==9935==    by 0x4448C1: hetplas::run(funkyPars*) (hetplas.cpp:207)
==9935==    by 0x457C59: interface(funkyPars*) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x457C78: slave(void*) (in /home/software/angsd/angsd0.591/angsd)
==9935==    by 0x9D0FF6D: start_thread (pthread_create.c:311)
==9935==    by 0xA83D9CC: clone (clone.S:113)
==9935==  Address 0x54 is not stack'd, malloc'd or (recently) free'd
==9935== 

1. -> If you really want angsd to exit uncleanly ctrl+c: 0 more times
2. fix ./angsd0.591.smartcount/angsd -i angsd0.591.smartcount/DNK02.hg19.flt.sort.rmdup.realign.md.bam -out tmp -minQ 20 -minMapQ 30 -P 2 does nothing but crashes
3. check that first line in .arg file is the command used
4. check domajorminor for -domaf complains about it lagging
5. fix -r problem if chromosome contains :
6. if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor
7. don't quit program if a chr is not included in the -sites file
8. check all getoptions stderr output.
9. -samglfclean not documented
10. soap usage is not documented
11. 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

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