Merge upstream into fork

.travis.yml

@@ -1,12 +1,11 @@
 language: c
 env:
-  - BRANCH=master
+  - BRANCH=devel
 
 before_install:
-  - export PATH="nim-$BRANCH/bin/nim/bin:${PATH:+:$PATH}"
   - export LD_LIBRARY_PATH=./htslib/
-  - export PATH="nim-$BRANCH/bin${PATH:+:$PATH}"
-  - export PATH="$(pwd)/nimble/src:$PATH"
+  - export PATH="$TRAVIS_BUILD_DIR/nim-$BRANCH/bin:$PATH"
+  - export NIM_LIB_PREFIX=$TRAVIS_BUILD_DIR/nim-$BRANCH/
 
 install:
   - bash ./scripts/install.sh
@@ -15,10 +14,6 @@ script:
   - bash functional-tests.sh
   - nim c -d:release --cc:$CC mosdepth.nim
   - ./mosdepth -h
-cache:
-  directories:
-    - nim-master
-    - nim-devel
 branches:
   except:
     - gh-pages

CHANGES.md

@@ -1,3 +1,18 @@
+0.2.5 (dev)
+=====
++ remove dependency on PCRE
+
+0.2.4
+=====
++ Add optional `--include-flag` to allow counting only reads that have some bits in the specified flag set.
+  This will only be used rarely--e.g. to count only supplemental reads, use `-F 0 --include-flag 2048`.
++ Fix case when only a single argument was given to --quantize
++ add --read-groups option to allow specifying that only certain read-groups should be used in the depth calculation. (#60)
++ add --fast-mode that does not look at internal cigar operations like (I)insertions or (D)eletions, but does consider soft and
+  hard-clips at the end of the alignment. Also does not correct for mate overlap. This makes mosdepth as much as **2X faster for 
+  CRAM** and is likely the desired mode for people using the depth for CNV or general coverage values as drops in coverage
+  due to CIGAR operations are often not of interest for coverage-based analyses.
+
 0.2.3
 =====
 + fix bug in region.dist with chromosomes in bam header, but without any reads. thanks (@vladsaveliev for reporting)

README.md

@@ -49,11 +49,14 @@ Common Options:
 Other options:
 
   -F --flag <FLAG>              exclude reads with any of the bits in FLAG set [default: 1796]
+  -i --include-flag <FLAG>      only include reads with any of the bits in FLAG set. default is unset. [default: 0]
+  -x --fast-mode                dont look at internal cigar operations or correct mate overlaps (recommended for most use-cases).
   -q --quantize <segments>      write quantized output see docs for description.
   -Q --mapq <mapq>              mapping quality threshold [default: 0]
   -T --thresholds <thresholds>  for each interval in --by, write number of bases covered by at
                                 least threshold bases. Specify multiple integer values separated
                                 by ','.
+  -R --read-groups <string>     only calculate depth for these comma-separated read groups IDs.
   -h --help                     show help
 
 ```
@@ -86,12 +89,16 @@ The distribution of depths will go to `sample-output.mosdepth.dist.txt`
 For 500-base windows
 
 ```
-mosdepth -n --by 500 sample.wgs $sample.wgs.bam
+mosdepth -n --fast-mode --by 500 sample.wgs $sample.wgs.cram
 ```
 
 `-n` means don't output per-base data, this will make `mosdepth`
 a bit faster as there is some cost to outputting that much text.
 
+--fast-mode avoids the extra calculations of mate pair overlap and cigar operations,
+and also allows htslib to extract less data from CRAM, providing a substantial speed
+improvement.
+
 ### Callable regions example
 
 To create a set of "callable" regions as in [GATK's callable loci tool](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_coverage_CallableLoci.php):
@@ -128,6 +135,12 @@ This also forces the output to have 5 decimals of precision rather than the defa
 
 The simplest way is to [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/mosdepth/README.html)
 
+It can also be installed with `brew` as `brew install brewsci/bio/mosdepth` or used via docker with quay:
+```
+docker pull quay.io/biocontainers/mosdepth:0.2.4--he527e40_0
+docker run -v /hostpath/:/opt/mount quay.io/biocontainers/mosdepth:0.2.4--he527e40_0 mosdepth -n --fast-mode -t 4 --by 1000 /opt/mount/sample /opt/mount/$bam
+```
+
 Unless you want to install [nim](https://nim-lang.org), simply download the
 [binary from the releases](https://github.com/brentp/mosdepth/releases).
 
@@ -156,6 +169,9 @@ Then pass that path to mosdepth just like we did with htslib
 LD_LIBRARY_PATH=~/src/pcre-8.41/.libs/:/~/src/htslib/ mosdepth -h
 ```
 
+If you still see an error about `could not import: pcre_free_study` then 
+for some, the solution has been to do: `ln -s /usr/local/lib/libpcre.so /usr/local/lib/libpcre.so.3`
+
 If you do want to install from source, see the [travis.yml](https://github.com/brentp/mosdepth/blob/master/.travis.yml)
 and the [install.sh](https://github.com/brentp/mosdepth/blob/master/scripts/install.sh).
 
@@ -166,8 +182,8 @@ If you use archlinux, you can [install as a package](https://aur.archlinux.org/p
 This is **useful for QC**.
 
 The `$prefix.mosdepth.global.dist.txt` file contains, a cumulative distribution indicating the
-proportion of total bases (or the proportion of the `--by` for `$prefix.mosdepth.region.dist.txt) that were covered
-for at least a given coverage value. It does this for each chromosom, and for then
+proportion of total bases (or the proportion of the `--by` for `$prefix.mosdepth.region.dist.txt`) that were covered
+for at least a given coverage value. It does this for each chromosome, and for the
 whole genome.
 
 Each row will indicate:

functional-tests.sh

@@ -11,7 +11,7 @@ test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest
 set -o nounset
 
 set -e
-nim c --boundChecks:off mosdepth.nim
+nim c --boundChecks:on -x:on mosdepth.nim
 set +e
 exe=./mosdepth
 bam=/data/human/NA12878.subset.bam
@@ -27,6 +27,14 @@ assert_equal "$(zgrep ^MT t.per-base.bed.gz)" "MT	0	80	1
 MT	80	16569	0"
 assert_equal "$(zgrep -w ^1 t.per-base.bed.gz)" "1	0	249250621	0"
 
+run overlapFastMode $exe t --fast-mode tests/ovl.bam
+assert_equal "$(zgrep ^MT t.per-base.bed.gz)" "MT	0	6	1
+MT	6	42	2
+MT	42	80	1
+MT	80	16569	0"
+assert_exit_code 0
+
+
 run missing_chrom $exe -c nonexistent --by 20000 t tests/ovl.bam
 assert_in_stderr "[mosdepth] chromosome nonexistent not found"
 assert_exit_code 1
@@ -54,6 +62,9 @@ assert_equal "$(zgrep ^MT t.quantized.bed.gz)" "MT	0	80	1:1000
 MT	80	16569	0:1"
 assert_equal "$(zgrep -w ^1 t.quantized.bed.gz)" "1	0	249250621	0:1"
 
+run single-quant $exe -q 60 t tests/nanopore.bam
+assert_exit_code 0
+
 
 rm -f t.thresholds.bed.gz*
 run threshold_test $exe --by 100 -T 0,1,2,3,4,5 -c MT t tests/ovl.bam
@@ -84,10 +95,21 @@ assert_exit_code 1
 assert_in_stderr "skipping bad bed line:MT	2"
 assert_in_stderr "invalid integer: asdf"
 
-run big_chrom $exe t tests/big.bam
+
+$exe -n t tests/ovl.bam
+run test_read_group $exe -n tt tests/ovl.bam -R GT04008021_119
+assert_equal $(cat tt.mosdepth.global.dist.txt | wc -l) 4 
+assert_equal $(diff tt.mosdepth.global.dist.txt t.mosdepth.global.dist.txt | wc -l) 0
 assert_exit_code 0
 
+run test_missing_read_group $exe -n tt tests/ovl.bam -R MISSING
+assert_equal "$(cat tt.mosdepth.global.dist.txt)" "MT	0	1.00
+total	0	1.00"
+
+run big_chrom $exe t tests/big.bam
+assert_exit_code 0
 
+rm -f tt.mosdepth.region.dist.txt
 rm -f t.mosdepth.region.dist.txt
 run empty_tids $exe t -n --thresholds 1,5 --by tests/empty-tids.bed tests/empty-tids.bam
 assert_exit_code 0