Haibao Tang
`apps.fetch` could switch to using REST API instead of Globus XML https://files.jgi.doe.gov/apidoc/
http://github.com/tanghaibao/quota-alignment/blob/master/cluster_utils.py#L139 Although quite uncommon - when extend is set to large a negative value - non-overlapping segments, after correcting the boundaries, can become overlapping. This is not intended behavior. For...
the quota enforces matching on the block level, may need to implement an additional round of matching within the block (strictly 1-to-1)
Based on Jingping's idea below: Since the program takes an existed tree and that tree construction itself can be fishy sometimes. I wonder if the algo might also try to...
Explore the alternative method, for example using STRUCTURE, this is explored in the following paper http://www.ncbi.nlm.nih.gov/pubmed/21472410 Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for...
Currently only two tests are performed on internal nodes, and quite simplistic: t-test (for continuous data), and Fisher's exact test (for categorical data). Study the theory behind this package: http://www.is.titech.ac.jp/~shimo/prog/pvclust/...
Dear, Thank you for the excellent plotting software. The setting `max_nb_lines` controls how many highest scoring alignments to include in the dot plot, and is fixed in the source code...
When running trimReads on many adapters, it crashes, with the error coming from the internal SeqAn procedure. ``` (gdb) bt #0 0x0000003e17873005 in _int_malloc () from /lib64/libc.so.6 #1 0x0000003e17874cde in...
`genomepy.Genome` helps with getting the sizes of contigs and also getting index. We should consolidate with `formats.sizes.SizesFile`.