Merge pull request #240 from smithlabcode/remove-unused-commands

Removing the lc command

Author: andrewdavidsmith

Makefile.am

@@ -51,7 +51,6 @@ EXTRA_DIST = \
              docs/content/hmr-rep.md \
              docs/content/hypermr.md \
              docs/content/index.md \
-             docs/content/lc.md \
              docs/content/levels.md \
              docs/content/liftfilter.md \
              docs/content/merge-bsrate.md \
@@ -220,7 +219,6 @@ dnmtools_SOURCES += src/utils/guessprotocol.cpp
 dnmtools_SOURCES += src/utils/uniq.cpp
 dnmtools_SOURCES += src/utils/merge-bsrate.cpp
 dnmtools_SOURCES += src/utils/format-reads.cpp
-dnmtools_SOURCES += src/utils/lc-approx.cpp
 dnmtools_SOURCES += src/utils/selectsites.cpp
 dnmtools_SOURCES += src/utils/symmetric-cpgs.cpp
 dnmtools_SOURCES += src/utils/merge-methcounts.cpp

docs/content/lc.md

@@ -42,7 +42,6 @@ nav:
    - General-purpose tools:
      - 'cleanhp': 'cleanhp.md'
      - 'guessprotocol': 'guessprotocol.md'
-     - 'lc': 'lc.md'
      - 'merge-bsrate': 'merge-bsrate.md'
      - 'merge': 'merge.md'
      - 'selectsites': 'selectsites.md'

docs/mkdocs.yml

@@ -114,8 +114,6 @@ main_format(int argc, const char **argv);
 int
 main_guessprotocol(int argc, const char **argv);
 int
-main_lc_approx(int argc, const char **argv);
-int
 main_lift_filter(int argc, const char **argv);
 int
 main_merge_bsrate(int argc, const char **argv);
@@ -202,7 +200,6 @@ main(int argc, const char **argv) {
 {"utilities",
  {{{"cleanhp",       "fix and stat invdup/hairping reads", main_clean_hairpins},
    {"guessprotocol", "guess whether protocol is ordinary, pbat or random", main_guessprotocol},
-   {"lc",            "approximate line counts in a file", main_lc_approx},
    {"merge-bsrate",  "merge bisulfite conversion rates files from bsrate", main_merge_bsrate},
    {"merge",         "merge multiple counts files into a counts file or a table", main_merge_methcounts},
    {"covered",       "filter a counts file for only covered sites", main_covered},