Add two params, min_align_count min_annots_in_align, to the reporting…

… in the summarize step
legumeinfo · Feb 27, 2024 · 1b2337b · 1b2337b
1 parent 947861f
commit 1b2337b
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/bin/pandagma-fam.sh b/bin/pandagma-fam.sh
@@ -892,9 +892,10 @@ run_clean() {
 ########################################
 # Main program
 
-pandagma_conf_params='clust_iden clust_cov extra_iden mcl_inflation strict_synt 
-ks_low_cutoff ks_hi_cutoff ks_binsize ks_block_wgd_cutoff max_pair_ks 
-consen_prefix annot_str_regex'
+pandagma_conf_params='clust_iden clust_cov extra_iden mcl_inflation strict_synt
+ks_low_cutoff ks_hi_cutoff ks_binsize ks_block_wgd_cutoff
+max_pair_ks min_align_count min_annots_in_align
+consen_prefix annot_str_regex preferred_annot expected_quotas'
 
 # The steps align_cds, align_protein, model_and_trim, calc_trees, and xfr_aligns_trees may be run separately.
 # Those steps (functions) are in pandagma-common.sh

diff --git a/config/family3_22_3.conf b/config/family3_22_3.conf
@@ -11,7 +11,7 @@ ks_block_wgd_cutoff="1.75"  # Fallback, if a ks_cutoffs file is not provided.
 max_pair_ks="4.0"    # Fallback value for excluding gene pairs, if a ks_cutoffs file is not provided.
 consen_prefix='Legume.fam3.'
 annot_str_regex='([^.]+\.[^.]+)\..+'
-min_align_count="6" # Minimum number of sequences in a family to trigger alignments, modeling, and trees
+min_align_count="4" # Minimum number of sequences in a family to trigger alignments, modeling, and trees
 min_annots_in_align="2" # Minimum number of distinct annotation groups in an alignment to retain it
 
 expected_quotas=(