Finished POD for all modules and programs

fortune9 · May 3, 2015 · e9db198 · e9db198
1 parent 1efa461
commit e9db198
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Showing 10 changed files with 721 additions and 105 deletions.
diff --git a/MANIFEST b/MANIFEST
@@ -1,34 +1,130 @@
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+.git/config
+.git/description
+.git/HEAD
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+.gitignore
 bin/build_cai_param.pl
 bin/build_tai_param.pl
 bin/calculate_CUB.pl
+bin/tmp1
 Changes
 ignore.txt
 lib/Bio/CUA.pm
 lib/Bio/CUA/CodonTable.pm
 lib/Bio/CUA/CUB.pm
-lib/Bio/CUA/CUB/Builder.pm
+lib/Bio/CUA/CUB/.Calculator.pm.swp
 lib/Bio/CUA/CUB/Calculator.pm
 lib/Bio/CUA/Seq.pm
 lib/Bio/CUA/SeqIO.pm
 lib/Bio/CUA/Summarizer.pm
-Makefile.PL
 MANIFEST			This list of files
+MANIFEST.bak
+MANIFEST.SKIP
 README
 t/00-load.t
+t/01-seqio.t
+t/02-codontable.t
+t/03-summarizer.t
+t/04-builder.t
+t/05-calculator.t
 t/b_CAI_param.S2_top_200.b1000
 t/build_cai_param.v1.0.pl
 t/build_tai_param.pl
+t/cai.out
 t/CAI_param.S2_top_200
 t/CAI_param.S2_top_200.by_avg
 t/dmel_r5_apr2006.tAI_param
+t/dmel_r5_apr2006.tRNA_copy
+t/expected.tsv
+t/generate_expected_data.pl
 t/longest_cds.fa.filtered
 t/longest_cds.stat_summary.S2.bCAI_t200_b1000
 t/manifest.t
 t/pod-coverage.t
 t/pod.t
 t/S2_RPKM.tsv
 t/summarize_cds_stat.pl
+t/tai.out
+t/test.fa
 t/tmp1
 t/tmp2
 t/tmp_positive
+TODO
 xt/boilerplate.t
diff --git a/MANIFEST.SKIP b/MANIFEST.SKIP
@@ -16,3 +16,4 @@ pod2htm*.tmp
 pm_to_blib
 Bio-CUA-*
 Bio-CUA-*.tar.gz
+.git/
diff --git a/TODO b/TODO
@@ -1,3 +1,4 @@
 I have the following in mind.
 
 1. add statistical methods to detect optimal codons.
+2. add graphic interface if under high demand.