{% if start_vars.tool_used == "Mapping" %}
Computing the Maps
Time Elapsed:
Trait Metadata
species =
{{ start_vars.species[0] | upper }}{{ start_vars.species[1:] }}
group =
{{ start_vars.group[0] | upper }}{{ start_vars.group[1:] }}
trait identifier =
{{ start_vars.trait_name }}
n of sample =
{{ start_vars.n_samples }}
{% if start_vars.transform != "" %}
transformation =
{{ start_vars.transform }}
{% endif %}
hash of sample values =
{{ start_vars.vals_hash }}
Mapping Metadata
mapping method =
{% if start_vars.method == "gemma" %}GEMMA {% if start_vars.use_loco == "True" %}using LOCO {% endif %}{% else %}{{ start_vars.method }}{% endif %}
{% if start_vars.maf != "" and start_vars.method != "reaper" %}
minor allele frequency lower limit =
{{ start_vars.maf }}
{% endif %}
{% if start_vars.covariates != "" and start_vars.method != "reaper" %}
{% set covariate_list = start_vars.covariates.split(",") %}
cofactors =
{% for covariate in covariate_list %}{% set this_covariate = covariate.split(":")[0] %}{{ this_covariate }}{% if not loop.last %}, {% endif %}{% endfor %}
{% else %}
cofactors =
None
{% endif %}
{% if start_vars.control_marker != "" and start_vars.do_control == "true" and start_vars.method != "gemma" %}
marker covariate =
{{ start_vars.control_marker }}
{% endif %}
{% if start_vars.genofile != "" %}
{% set genofile_desc = start_vars.genofile.split(":")[1] %}
genotype file =
{{ genofile_desc }}
{% else %}
genotype file =
{{ start_vars.group[0] | upper }}{{ start_vars.group[1:] }}.geno
{% endif %}
{% if start_vars.num_perm | int > 0 and start_vars.method != "gemma" %}
n of permutations =
{{ start_vars.num_perm }}
{% endif %}
{% if num_bootstrap in start_vars %}
{% if start_vars.num_bootstrap | int > 0 and start_vars.method == "reaper" %}
n of bootstrap =
{{ start_vars.num_bootstrap }}
{% endif %}
{% endif %}
{% else %}
{{ start_vars.tool_used }} Computation in progress ...
{% endif %}
{% if start_vars.vals_diff|length != 0 and start_vars.transform == "" %}
| Sample |
New Value |
Old Value |
{% for sample in start_vars.vals_diff %}
| {{ sample }} |
{{ start_vars.vals_diff[sample].new_val }} |
{{ start_vars.vals_diff[sample].old_val }} |
{% endfor %}
{% endif %}