ole-tange/barmaids

Issues

• bammds_parallel

  #98 opened 10 years ago by sapfo
  6

• update http://savannah.nongnu.org/projects/bammds/

  #100 opened 10 years ago by sapfo
  0

• update the article citation in the verbose

  #99 opened 10 years ago by sapfo
  0

• Legend file: duplicate name NGS and reference panel...

  #97 opened 11 years ago by sapfo
  0

• paper submission: what is needed

  #95 opened 11 years ago by sapfo
  4

• bamdamage: need to rewrite this script. it contains notably a bug with regard to Ns.

  #65 opened 11 years ago by sapfo
  16

• R is a memory pig, so the bammds_plot.r cannot run on small machines

  #92 opened 11 years ago by ole-tange
  14

• summary of number of snps: slow when rerunning

  #89 opened 11 years ago by sapfo
  11

• pdf output file for publication

  #90 opened 11 years ago by sapfo
  12

• Runtimes and memory use for different runs

  #96 opened 11 years ago by ole-tange
  7

• bug: when the snps are not ordered, the samtools pileup crashes

  #88 opened 11 years ago by sapfo
  9

• Ordering, duplicated names in the legend file

  #91 opened 11 years ago by sapfo
  9

• bammds: Warning: Not overwriting legend.csv duplicated

  #93 opened 11 years ago by sapfo
  7

• Test parallel --round-robin

  #94 opened 11 years ago by ole-tange
  1

• on eos, lemaitre: problem with R: no output is being generated

  #74 opened 11 years ago by sapfo
  5

• doc directory and *4mac files not packed

  #86 opened 11 years ago by morenomayar
  7

• bamdamage man page

  #87 opened 11 years ago by ole-tange
  2

• Test bammds on watt

  #84 opened 11 years ago by ole-tange
  5

• parent.pm library

  #78 opened 11 years ago by morenomayar
  4

• simulations: timing

  #53 opened 11 years ago by sapfo
  2

• simulations: new ancient genome

  #83 opened 11 years ago by ole-tange
  1

• Create webpage under newton: dna.ku.dk/~sapfo/bammds

  #85 opened 11 years ago by ole-tange
  5

• simulations: describe centroid etc in the ms

  #82 opened 11 years ago by ole-tange
  1

• output on the screen: by default too much info?

  #76 opened 11 years ago by sapfo
  7

• configure & make dist-gz: help installing fatpack

  #79 opened 11 years ago by sapfo
  2

• Update man page with correct input file order

  #80 opened 11 years ago by mortenr
  4

• Filling up /tmp

  #72 opened 11 years ago by morenomayar
  5

• pca, mds: are we still outputing both by default?

  #77 opened 11 years ago by sapfo
  7

• Long names not working

  #70 opened 11 years ago by morenomayar
  7

• simulations: correct region assignment

  #81 opened 11 years ago by ole-tange
  1

• on eos, lemaitre: no manual page

  #75 opened 11 years ago by sapfo
  3

• add mike to ped format converter etc

  #73 opened 11 years ago by morenomayar
  2

• bam against bam does not work

  #60 opened 11 years ago by morenomayar
  3

• configure & make install: for macs

  #69 opened 11 years ago by sapfo
  2

• Very high proportion of triallelic sites with different ref datasets !!!!!!!

  #61 opened 11 years ago by morenomayar
  11

• Some file formats give more markers than expected

  #64 opened 11 years ago by ole-tange
  8

• small bugs

  #68 opened 11 years ago by sapfo
  6

• csv output not working

  #71 opened 11 years ago by morenomayar
  1

• rmpop/rmind: do we still have that in?

  #66 opened 11 years ago by sapfo
  7

• dim1 and dim2 as alias for xvector/yvector

  #67 opened 11 years ago by ole-tange
  1

• chromosome: could be any word..check for that?

  #52 opened 11 years ago by sapfo
  1

• clean the directory for old files etc

  #51 opened 11 years ago by sapfo
  1

• Read file in R is slow

  #56 opened 11 years ago by ole-tange
  2

• Installation guide

  #63 opened 11 years ago by ole-tange
  1

• Report which kind of sites are triallelic

  #62 opened 11 years ago by ole-tange
  1

• bammds crashes when running on a different bam file

  #57 opened 11 years ago by sapfo
  5

• Speed up summing by using --round-robin

  #59 opened 11 years ago by ole-tange
  2

• Does the order of markers in the ASD-file matter?

  #58 opened 11 years ago by ole-tange
  1

• bammds testinputfiles/batch_31.vcf -m 30 -n 20

  #55 opened 11 years ago by sapfo
  2

• empty asdfile: crash, dont run the plotting part and output an error message?

  #54 opened 11 years ago by sapfo
  1