Merge branch 'master' of github.com:smithlabcode/dnmtools into selectsites-input-file-type

Author: andrewdavidsmith

Makefile.am

@@ -66,8 +66,8 @@ EXTRA_DIST = \
              data/radmeth_test_design.txt \
              data/two_epialleles.states \
              data/araTha1_simulated.counts.gz \
+             data/mlml_test_data.tgz \
              test_scripts/test_abismalidx.test \
-             test_scripts/test_simreads.test \
              test_scripts/test_abismal.test \
              test_scripts/test_format.test \
              test_scripts/test_uniq.test \
@@ -82,7 +82,8 @@ EXTRA_DIST = \
              test_scripts/test_states.test \
              test_scripts/test_amrfinder.test \
              test_scripts/test_hypermr.test \
-             test_scripts/test_diff.test
+             test_scripts/test_diff.test \
+             test_scripts/test_mlml.test
 
 ### ADS: the file md5sum.txt can be regenerated by running the tests
 ### with "make check" and then doing `md5sum tests/* > md5sum.txt`
@@ -96,8 +97,15 @@ AM_CPPFLAGS = -I $(top_srcdir)/src/common -I $(top_srcdir)/src/smithlab_cpp -I $
 
 CXXFLAGS = -Wall -O3 $(OPENMP_CXXFLAGS) # default has optimization on
 
-TESTS = test_scripts/test_simreads.test \
-        test_scripts/test_abismalidx.test \
+### ADS: Testing with `make check` can be a long process. Testing with
+### `make check` is designed to work recursively. Modifying this
+### behavior requires overriding build-in rules which generates
+### warnings, probably for good reason. Defining a check-local only
+### adds to functionality and does not remove the dependency that
+### causes the recursion. The preferred alternative is to do `make`
+### first and then `make check-TESTS` after. This will not do tests
+### recursively.
+TESTS = test_scripts/test_abismalidx.test \
         test_scripts/test_abismal.test \
         test_scripts/test_format.test \
         test_scripts/test_uniq.test \
@@ -112,7 +120,8 @@ TESTS = test_scripts/test_simreads.test \
         test_scripts/test_states.test \
         test_scripts/test_amrfinder.test \
         test_scripts/test_hypermr.test \
-        test_scripts/test_diff.test
+        test_scripts/test_diff.test \
+        test_scripts/test_mlml.test
 
 TEST_EXTENSIONS = .test
 
@@ -230,13 +239,12 @@ CLEANFILES = \
     tests/reads.mstats \
     tests/reads.sam \
     tests/reads.ustats \
-    tests/simreads_1.fq \
-    tests/simreads_2.fq \
     tests/tRex1.idx \
     tests/tRex1_promoters.roi.bed \
     tests/reads.counts.select \
     tests/radmeth_test_output.txt \
     tests/reads.epiread \
     tests/two_epialleles.amr \
     tests/araTha1_simulated.hypermr \
-    tests/methylome_ab.diff
+    tests/methylome_ab.diff \
+    tests/mlml.out

configure.ac

@@ -75,6 +75,7 @@ tests/two_epialleles.states:data/two_epialleles.states
 tests/araTha1_simulated.counts.gz:data/araTha1_simulated.counts.gz
 tests/methylome_a.counts.sym:data/methylome_a.counts.sym
 tests/methylome_b.counts.sym:data/methylome_b.counts.sym
+tests/mlml_test_data.tgz:data/mlml_test_data.tgz
 ])
 
 AC_OUTPUT

data/md5sum.txt

@@ -1,22 +1,21 @@
 ae05a28de5643a512386e767b3aa963a  tests/araTha1_simulated.hypermr
 0048de3fc412cb12ec2e070c8151f86f  tests/methylome_ab.diff
 86ca23015535cf3295c0da3587a95f22  tests/radmeth_test_output.txt
-575f7daf8062c4aa3194370488794be8  tests/reads.bsrate
-68cc65a337d5529295c813f282665dfe  tests/reads.counts
-1f29966bbbc11985f724c8e0c0f1db2b  tests/reads.counts.select
-34f5eddd80d5d35131f92697d4cca896  tests/reads.counts.sym
-5f6bd7100470c5306b41b6a56fe6690e  tests/reads.epiread
-97508d22db32305d4688db8374d1a04a  tests/reads.fmt.sam
-6de21c61705040072be76cddae481cfa  tests/reads.fmt.srt.sam
-1cf51932cef739544b91a41bdfdb8841  tests/reads.fmt.srt.uniq.sam
-103225f9a3adc45836e366551989909b  tests/reads.hmr
-3cbec246887d1837f004e4643148f7e6  tests/reads.levels
-3bf209c27c99134386ea63756ff9fe2c  tests/reads.mstats
-7a02c7d93111403a4619ccc74aa3c78e  tests/reads.sam
-b067a733102e611ca614ae22fc944471  tests/reads.ustats
-8e5ad0faefe241de9c2c5748e005e2e8  tests/simreads_1.fq
-4ebacfec717182fafce46b037591b228  tests/simreads_2.fq
-3ba5a1c4c420ca7a2dbd88290033c3bc  tests/tRex1.idx
-b5270bb38d798741cfa74f411a0d49bf  tests/tRex1_promoters.roi.bed
+6d513eed25f5c3da87252d8f6f816246  tests/reads.bsrate
+8dfe79399d873da3d1749eaabf7581e2  tests/reads.counts
+961b0671a349e2ad8041e0807393bf78  tests/reads.counts.select
+af22e5468fd6614c611646cbc675542f  tests/reads.counts.sym
+b38d571baaf2bc16646dbd14a7edb770  tests/reads.epiread
+6abb0e3e6571e221ec6f91ba52a358ea  tests/reads.fmt.sam
+8edab98b1be4411820e2f130aa6ba6b9  tests/reads.fmt.srt.sam
+3e57d7bde5f7be88b56cd92bbfc935ce  tests/reads.fmt.srt.uniq.sam
+af8b97ef25af8a16ced1537ca4a74d07  tests/reads.hmr
+52d44c4c1d6891b45741f573f51e67cd  tests/reads.levels
+916fe07a1d03449b65dfc1458d7c1c40  tests/reads.mstats
+65816bee34b977adf1dd798fbf85d758  tests/reads.sam
+1aecbb2b12bd867405118eae42de6743  tests/reads.ustats
+bcbf01be810cbf4051292813eb6b9225  tests/tRex1.idx
+7c84dafb85252a04a45704da71eba7c4  tests/tRex1_promoters.roi.bed
 e7e9590475a7f9b1ae41701d81892e57  tests/two_epialleles.amr
 ec6a686617cad31e9f7a37a3d378e6ed  tests/two_epialleles.states
+93e38b20d162062a5d147c4290095a13  tests/mlml.out

data/mlml_test_data.tgz

@@ -19,15 +19,15 @@ pip install -U mkdocs
 
 Build the HTML documentation by running
 ```
-mkdocs build
+mkdocs build -f docs/mkdocs.yml
 ```
 which will create a `site` directory where markdown files are
 converted to HTML
 
 Create a local host for the HTML documentation by running
 
 ```
-mkdocs serve
+mkdocs serve -f docs/mkdocs.yml
 ```
 
 This will create the documentation, usually at http://localhost:8000 .

docs/README.md

@@ -136,7 +136,42 @@ Use only reads that map to this chromosome (e.g. chrM). This simply
 avoids having to extract reads separately from the mapped reads file
 before using bsrate.
 
+```txt
+ -A, -a-rich
+```
+The reads are A-rich. This may be relevant if a BPAT protocol is used.
+
 ```txt
 -v, -verbose
 ```
 Print more information while the program is running.
+
+```txt
+ -S, -summary
+```
+Write the analysis summary to this file. The summary is not reported
+unless a file is specified here. This information includes nothing
+beyond what is currently generated for the output file. This option is
+correct as of v1.4.0.
+
+```txt
+ -t, -threads
+```
+Use this many threads. This only has an effect if set to a value
+greater than 1. The additional threads are only used for decompressing
+BAM format input. It is not recommended to use many threads due to
+diminishing returns, and performance will degrade if more threads are
+specified than physical cores available. This option is correct as of
+v1.4.0.
+
+```txt
+ -p, -per-read
+```
+This option will generate a histogram of conversion rate per read,
+printed to the terminal. This option is correct as of v1.4.0.
+
+```txt
+ -p, -per-read
+```
+Assming the `-p` option is used, this option determines the number of
+bins in the histogram. This option is correct as of v1.4.0.

docs/content/bsrate.md

@@ -38,6 +38,11 @@ in `input-a.meth`, number of unmethylated reads in `input-a.meth`,
 number of methylated reads in `input-b.meth`, and number of
 unmethylated reads in `input-b.meth`, respectively.
 
+The two input files must be have all sites within a chromosomes
+consecutive, have the same chromosome order, and have sites sorted in
+increasing order within each chromosome. The order of chromosomes does
+not matter (e.g., chr10 may precede chr2, or chr2 may precede chr10).
+
 **Warning** the order of the samples/methylomes given as input, the
 "a" and "b", matters. It is probably a good idea to include this order
 in the output file name, for example as `output_a_lt_b.diff`.

docs/content/diff.md

@@ -170,3 +170,9 @@ File in which to write parameters learned during the current run.
 A random number seed. Randomization is used in a shuffling step prior
 to filering candidate HMRs. This parameter is typically only used for
 testing (default: 408).
+
+```txt
+ -S, -summary
+```
+Write the analysis summary to this file. The summary is not
+reported unless a file is specified here. This option is correct as of v1.4.0.

docs/content/hmr.md

@@ -186,3 +186,10 @@ Write the trained parameters to this file.
  -s, -seed
 ```
 Specify a random seed value.
+
+```txt
+ -S, -summary
+```
+Write the analysis summary to this file. The summary is not
+reported unless a file is specified here. This option is correct as of v1.4.0.
+

docs/content/pmd.md

@@ -49,10 +49,10 @@ most helpful when the input and output are both BAM, where the threads
 can really speed things up.
 
 ```txt
- -S, -stats
+ -S, -summary
 ```
 Save statistics on duplication rates to this file. The statistics are not
-reported unless a file is specified here.
+reported unless a file is specified here. This option is correct as of v1.4.0.
 
 ```txt
  -hist