Merge branch 'main' of github.com:telatin/bamtocov into main

.github/workflows/build.yml

@@ -49,21 +49,17 @@ jobs:
         sudo apt-get update
         sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
              curl libssl-dev libtool autoconf automake libcurl4-openssl-dev
-
-    # Setup htslib
     - name: Install htslib (linux)
       if: runner.os == 'Linux'
       run: |
         cd
         git clone --recursive https://github.com/samtools/htslib.git
-        cd htslib && git checkout 1.12 && autoheader && autoconf && ./configure --enable-libcurl
-        cd
-        sudo make -j 4 -C htslib install
+        cd htslib && git checkout 1.11 && autoheader && autoconf && ./configure --enable-libcurl
+        sudo make -j 4 install
+        sudo ldconfig
         #echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
-        echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/htslib" >> $GITHUB_ENV
-        ls -lh $HOME/htslib/*.so
- 
-
+        #ls -lh $HOME/htslib/*.so
+        
     - name: Install hstlib (macos)
       if: runner.os == 'macOS'
       run: |
@@ -73,11 +69,6 @@ jobs:
       with:
         version: ${{ matrix.nimversion }}
 
-#    - uses: actions-rs/toolchain@v1
-#      with:
-#        toolchain: stable
-#    - uses: actions-rs/cargo@v1
-
 
     # Build and Test
     - name: Build macOS executable

.gitignore

@@ -27,3 +27,6 @@ _data/
 bin/covtotarget
 bin/gff2bed
 trash
+static/
+hts_nim_static_builder
+bin/*

Makefile

@@ -2,20 +2,37 @@
 .PHONY: testshpec testshunit2 test clean build
 
 BIN=./bin
+BIN2=./static
 SOURCE=./src
+LIBPATH=$(shell dirname $(shell which samtools) | sed 's/bin/lib/')
 NIM_PATHS= --colors:on --noNimblePath --path:/local/giovanni/bamtocov/nimbledeps/pkgs/hts-0.3.17 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/docopt-0.6.8 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/regex-0.19.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/unicodedb-0.9.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/lapper-0.1.7 
 VERSION := $(shell grep version bamtocov.nimble  | grep  -o "[0-9]\\+\.[0-9]\.[0-9]\\+")
 LIST=$(BIN)/bamtocov $(BIN)/bamtocounts $(BIN)/covtotarget $(BIN)/bamcountrefs $(BIN)/gff2bed $(BIN)/bamtocounts_legacy $(BIN)/bamtarget
+STATIC=$(BIN2)/bamtocov $(BIN2)/bamtocounts $(BIN2)/covtotarget $(BIN2)/bamcountrefs $(BIN2)/gff2bed $(BIN2)/bamtocounts_legacy $(BIN2)/bamtarget
+
 
 $(BIN)/%: $(SOURCE)/%.nim $(SOURCE)/covutils.nim bamtocov.nimble
 	nim c  $(NIM_PATHS) -d:NimblePkgVersion=$(VERSION) -d:release --opt:speed  --out:$@ $<
 
 all: $(LIST)
 
+./hts_nim_static_builder:
+	wget "https://github.com/brentp/hts-nim/releases/download/v0.2.8/hts_nim_static_builder"
+	chmod +x hts_nim_static_builder
+
+static: $(STATIC)
 
-test: testshpec 
+
+$(BIN2)/%: $(SOURCE)/%.nim bamtocov.nimble ./hts_nim_static_builder
+	mkdir -p $(BIN2)
+	echo target: $@
+	echo base: $(shell basename $@)
+	./hts_nim_static_builder  -n bamtocov.nimble -s $< -- -d:NimblePkgVersion=2.7.0
+	mv ./$(shell basename $@) $(BIN2)
+test: testshpec
 
 testall: testbash testshpec testshunit2
+
 testshpec:
 	@echo " --- Test shpec --- "
 	./tests/bin/shpec ./tests/shpec/bamtocov.sh

bamtocov.nimble

@@ -1,6 +1,6 @@
 # Package
 
-version       = "2.7.0"
+version       = "2.8.0"
 author        = "Andrea Telatin, Giovanni Birolo"
 description   = "BAM to Coverage"
 license       = "MIT"

datasets/physical/target.bed

@@ -0,0 +1,3 @@
+filt.1	1	100	test
+filt.1	101	250	test2
+filt.1	300	350	out

datasets/ref/ref-250.fa.fai

@@ -0,0 +1 @@
+filt.1	250	9	250	251

docs/tools/bamtocounts.md

@@ -14,7 +14,7 @@ more than once.
 ## Help screen
 
 ```text
-BamToCounts 2.5.0
+BamToCounts 2.7.0
 
   Usage: bamtocounts [options] <Target> <BAM-or-CRAM>...
 
@@ -26,9 +26,11 @@ Arguments:
 Options:
 
   -T, --threads <threads>      BAM decompression threads [default: 0]
-  -r, --fasta <fasta>          FASTA file for use with CRAM files [default: ].
+  -r, --fasta <fasta>          FASTA file for use with CRAM files [default: ]
   -F, --flag <FLAG>            Exclude reads with any of the bits in FLAG set [default: 1796]
   -Q, --mapq <mapq>            Mapping quality threshold [default: 0]
+  --paired                     Count read pairs rather than single reads
+  --strict                     Read must be contained, not just overlap, with feature
   --stranded                   Print strand-specific counts
   --coords                     Also print coordinates of each feature
 
@@ -40,6 +42,7 @@ Options:
   -l, --norm-len               Add a counts/length column (after RPKM when both used)
   -p, --precision INT          Digits for floating point precision [default: 3]
   --header                     Print header
+  --verbose                    Print verbose output
   --debug                      Enable diagnostics    
   -h, --help                   Show help
 ```
@@ -96,4 +99,4 @@ Adding `--stranded` and `--coords`:
 feature_1       seq1    100     200     7       0
 feature_2       seq1    300     400     0       7
 second_half     seq1    500     1000    0       0
-```
+```

input/phi/phi.fa.fai

@@ -0,0 +1 @@
+NC_001422.1	5386	49	70	71

src/bamtocov.nim

@@ -179,7 +179,21 @@ type
   coverage_interval_t = genomic_interval_t[tuple[l1: coverage_t, l2: string]] # l2 is the target interval or the chromosome
   #coverage_end_t = tuple[stop: pos_t, rev: bool]
   #coverage_t = tuple[forward, reverse: int]
-
+proc getReadEnd(start, stop, reflen: pos_t, extend: int): pos_t =
+  if extend == 0:
+    return stop
+  elif start < stop:
+    if start + extend > reflen:
+      return reflen
+    else:
+      return start + extend
+  else:
+    # start > stop
+    if stop - extend < 0:
+      return 0
+    else:
+      return stop - extend
+
 proc coverage_iter(bam: Bam, opts: input_option_t, target: target_t): iterator(): coverage_interval_t =
   result = iterator(): coverage_interval_t {.closure.} =
     var
@@ -245,10 +259,8 @@ proc coverage_iter(bam: Bam, opts: input_option_t, target: target_t): iterator()
         # increment coverage with aln starting here
         while more_alignments_for_ref and (next_change == aln.start):
           # EXP: --extendRead INT
-          let readEnd = if opts.extendFrag > 0: 
-                          if aln.start + opts.extendFrag > reflen: reflen
-                          else: aln.start + opts.extendFrag
-                        else: aln.stop
+          let readEnd = getReadEnd(aln.start, aln.stop, reflen, opts.extendFrag)
+
           coverage_ends.push(covEnd(stop: readEnd, reverse: aln.label))
           cov.inc(aln.label)
           if debug: stderr.writeLine("Added aln: " & $aln)
@@ -332,7 +344,8 @@ proc output_wig_span(span: genomic_interval_t[coverage_t], opts: output_option_t
       case opts.span_func:
         of sf_max, sf_min: $tot
         of sf_mean: $(float(tot)/float(span_length))
-  echo $span.start & "\t" & value_str
+  #echo $span.start & "\t" & value_str
+  echo value_str
 
 
 
@@ -804,4 +817,4 @@ when isMainModule:
     stderr.writeLine( "Quitting.")
   except:
     stderr.writeLine( getCurrentExceptionMsg() )
-    quit(1)   
+    quit(1)