[med-svn] [Git][med-team/bedtools][master] Remove the need for samtools via patch from upstream.
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Oct 28 10:58:17 GMT 2020
Michael R. Crusoe pushed to branch master at Debian Med / bedtools
Commits:
fdd46803 by Michael R. Crusoe at 2020-02-14T16:53:00+01:00
Remove the need for samtools via patch from upstream.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/no-samtools
- debian/patches/series
- debian/tests/control
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+bedtools (2.29.2+dfsg-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Remove the need for samtools via patch from upstream.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 14 Feb 2020 16:50:58 +0100
+
bedtools (2.29.2+dfsg-3) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -8,8 +8,7 @@ Build-Depends: debhelper-compat (= 12),
python3,
zlib1g-dev,
libbz2-dev,
- liblzma-dev,
- samtools (>= 1.10)
+ liblzma-dev
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/bedtools
Vcs-Git: https://salsa.debian.org/med-team/bedtools.git
@@ -19,7 +18,6 @@ Package: bedtools
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
-Recommends: samtools (>= 1.10)
Conflicts: filo
Provides: filo
Replaces: filo
=====================================
debian/patches/no-samtools
=====================================
@@ -0,0 +1,600 @@
+From: John Marshall <John.W.Marshall at glasgow.ac.uk>
+Date: Tue, 16 Apr 2019 11:48:55 +0100
+Subject: Use new htsutil.cpp in test suite instead of samtools
+Forwarded: https://github.com/arq5x/bedtools2/pull/818
+--- bedtools.orig/.github/workflows/main.yml
++++ bedtools/.github/workflows/main.yml
+@@ -9,8 +9,6 @@
+
+ steps:
+ - uses: actions/checkout at v1
+- - name: Install samtools
+- run: sudo apt-get install -y samtools
+ - name: Compile and test Bedtools
+ run: make -j8 && make test
+ - name: Compile static binary
+--- bedtools.orig/.gitignore
++++ bedtools/.gitignore
+@@ -12,12 +12,16 @@
+ .cproject
+ nbproject
+ sandbox
++test/coverage/*.bam
++test/coverage/*.bam.bai
+ test/general/o
+ test/genomecov/chip.bam
++test/genomecov/merged.bam
+ test/genomecov/one_block.bam
+ test/genomecov/pair-chip.bam
+ test/genomecov/sam-w-del.bam
+ test/genomecov/three_blocks.bam
++test/htsutil
+ test/multicov/one_block.bam.bai
+ test/multicov/two_blocks.bam.bai
+ test/genomecov/two_blocks.bam
+--- bedtools.orig/Makefile
++++ bedtools/Makefile
+@@ -130,7 +130,7 @@
+ ALL_LIBS = $(BT_LIBS) $(LIBS)
+
+
+-all: print_banner $(BIN_DIR)/bedtools $(BIN_DIR)/intersectBed
++all: print_banner $(BIN_DIR)/bedtools $(BIN_DIR)/intersectBed test/htsutil
+
+ static: print_banner $(BIN_DIR)/bedtools.static
+
+@@ -163,6 +163,9 @@
+ $(OBJ_DIR)/bedtools.o: $(SRC_DIR)/bedtools.cpp $(OBJ_DIR)/bedtools.d
+ $(CXX_COMPILE)
+
++$(OBJ_DIR)/htsutil.o: $(SRC_DIR)/htsutil.cpp $(OBJ_DIR)/htsutil.d
++ $(CXX_COMPILE)
++
+ # HTSlib's htslib.mk provides rules to rebuild $(HTSDIR)/libhts.a.
+ HTSDIR = src/utils/htslib
+ include $(HTSDIR)/htslib.mk
+@@ -181,6 +184,9 @@
+ $(CCPREFIX) $(CC_WRAPPER) $(CXX) -static $(ALL_LDFLAGS) -o $(BIN_DIR)/bedtools.static $(BUILT_OBJECTS) $(HTSDIR)/libhts.a $(ALL_LIBS)
+ @echo "done."
+
++test/htsutil: $(OBJ_DIR)/htsutil.o $(HTSDIR)/libhts.a
++ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_LDFLAGS) -o test/htsutil $(OBJ_DIR)/htsutil.o $(HTSDIR)/libhts.a $(ALL_LIBS)
++
+ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+ @echo "- Creating executables for old CLI."
+ @python3 scripts/makeBashScripts.py
+@@ -211,7 +217,7 @@
+ # not existing), so clean should also remove the generated config.h.
+ clean:
+ @echo " * Cleaning up."
+- @rm -f $(VERSION_FILE) $(OBJ_DIR)/* $(BIN_DIR)/*
++ @rm -f $(VERSION_FILE) $(OBJ_DIR)/* $(BIN_DIR)/* test/htsutil
+ @cd src/utils/htslib && make clean > /dev/null
+ @test -e src/utils/htslib/config.mk || rm -f src/utils/htslib/config.h
+ .PHONY: clean
+--- /dev/null
++++ bedtools/src/htsutil.cpp
+@@ -0,0 +1,167 @@
++#include <fstream>
++#include <iostream>
++#include <string>
++
++#include <htslib/bgzf.h>
++#include <htslib/sam.h>
++
++int convert(htsExactFormat outformat, const char *outfname, bool outheaders,
++ htsExactFormat informat, const char *infname,
++ const char *reffname = NULL)
++{
++ htsFile* in = NULL;
++ htsFile* out = NULL;
++ bam_hdr_t* hdr = NULL;
++ bam1_t* b = NULL;
++
++ try {
++ in = hts_open(infname, "r");
++ if (in == NULL)
++ throw std::string("can't open ") + infname;
++
++ if (hts_get_format(in)->format != informat)
++ throw std::string(infname) + ": file is in the wrong format";
++
++ const char *outf = "w";
++ switch (outformat) {
++ case sam: outf = "w"; break;
++ case bam: outf = "wb"; break;
++ case cram: outf = "wc"; break;
++ default: throw std::string("invalid outformat argument");
++ }
++
++ out = hts_open(outfname, outf);
++ if (out == NULL)
++ throw std::string("can't write to ") + outfname;
++
++ if (reffname) {
++ hts_set_fai_filename(in, reffname);
++ hts_set_fai_filename(out, reffname);
++ }
++
++ hdr = sam_hdr_read(in);
++ if (hdr == NULL)
++ throw std::string("can't read headers from ") + infname;
++
++ if (outheaders) {
++ if (sam_hdr_write(out, hdr) < 0)
++ throw std::string("can't write headers to ") + outfname;
++ }
++
++ int ret;
++ b = bam_init1();
++ while ((ret = sam_read1(in, hdr, b)) >= 0) {
++ if (sam_write1(out, hdr, b) < 0)
++ throw std::string("can't write record to ") + outfname;
++ }
++ if (ret < -1)
++ throw std::string("truncated input file");
++
++ bam_destroy1(b);
++ bam_hdr_destroy(hdr);
++ hts_close(out);
++ hts_close(in);
++ }
++ catch (const std::string& what) {
++ std::cerr << "htsutil: " << what << '\n';
++ bam_destroy1(b);
++ bam_hdr_destroy(hdr);
++ if (out) hts_close(out);
++ if (in) hts_close(in);
++ return 1;
++ }
++
++ return 0;
++}
++
++int compress(const char *outfname, std::streambuf* in)
++{
++ BGZF* out = NULL;
++
++ try {
++ out = bgzf_open(outfname, "w");
++ if (out == NULL)
++ throw std::string("can't write to ") + outfname;
++
++ char buffer[65536];
++ size_t n;
++ while ((n = in->sgetn(buffer, sizeof buffer)) > 0) {
++ if (bgzf_write(out, buffer, n) < 0)
++ throw std::string("can't write to ") + outfname;
++ }
++
++ bgzf_close(out);
++ }
++ catch (const std::string& what) {
++ std::cerr << "htsutil: " << what << '\n';
++ if (out) bgzf_close(out);
++ return 1;
++ }
++
++ return 0;
++}
++
++int compress(const char *outfname, const char *infname)
++{
++ if (std::string(infname) == "-")
++ return compress(outfname, std::cin.rdbuf());
++ else {
++ std::filebuf in;
++ if (in.open(infname, std::ios::in) == NULL) {
++ std::cerr << "htsutil: can't open " << infname << '\n';
++ return 1;
++ }
++ return compress(outfname, &in);
++ }
++}
++
++int index(const char *fname, bool csi)
++{
++ if (std::string(fname) == "-") {
++ std::cerr << "htsutil: can't index standard output\n";
++ return 1;
++ }
++
++ int ret = sam_index_build(fname, csi? 14 : 0);
++ if (ret < 0) return -ret; // Convert to exit status
++ return 0;
++}
++
++int main(int argc, char **argv)
++{
++ std::string cmd = (argc >= 2)? argv[1] : "--help";
++ const char *src = (argc >= 3)? argv[2] : "-";
++ const char *dest= (argc >= 4)? argv[3] : "-";
++
++ if (cmd == "viewbamrecords")
++ return convert(sam, "-", false, bam, src);
++ else if (cmd == "viewbam")
++ return convert(sam, "-", true, bam, src);
++ else if (cmd == "viewcramrecords")
++ return convert(sam, "-", false, cram, src, (argc >= 4)? argv[3] : NULL);
++ else if (cmd == "bgzfcompress")
++ return compress(dest, src);
++ else if (cmd == "index")
++ return index(src, false);
++ else if (cmd == "indexcsi")
++ return index(src, true);
++ else if (cmd == "samtobam")
++ return convert(bam, dest, true, sam, src);
++ else if (cmd == "samtoindexedbam") {
++ int ret = convert(bam, dest, true, sam, src);
++ if (ret != 0) return ret;
++ return index(dest, false);
++ }
++ else {
++ std::cerr <<
++"Usage: htsutil bgzfcompress [SRCFILE [DESTFILE]]\n"
++" htsutil index FILE\n"
++" htsutil indexcsi FILE\n"
++" htsutil samtobam [SRCFILE [DESTFILE]]\n"
++" htsutil samtoindexedbam SRCFILE DESTFILE\n"
++" htsutil viewbam [FILE]\n"
++" htsutil viewbamrecords [FILE]\n"
++" htsutil viewcramrecords [FILE [REFFILE]]\n";
++ return 1;
++ }
++}
+--- bedtools.orig/test/bamtobed/test-bamtobed.sh
++++ bedtools/test/bamtobed/test-bamtobed.sh
+@@ -18,13 +18,13 @@
+ # BAM files #
+ ###########################################################
+ ###########################################################
+-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
+-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
+-samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null
+-#samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null
+-samtools view -Sb two_blocks_w_D.sam > two_blocks_w_D.bam 2>/dev/null
+-samtools view -Sb numeric_tag.sam > numeric_tag.bam 2> /dev/null
+-gzip -dfc extra-long-header.sam | samtools view -Sb > extra-long-header.bam 2> /dev/null
++../htsutil samtobam one_block.sam one_block.bam
++../htsutil samtobam two_blocks.sam two_blocks.bam
++../htsutil samtobam three_blocks.sam three_blocks.bam
++#../htsutil samtobam sam-w-del.sam sam-w-del.bam
++../htsutil samtobam two_blocks_w_D.sam two_blocks_w_D.bam
++../htsutil samtobam numeric_tag.sam numeric_tag.bam
++gzip -dfc extra-long-header.sam | ../htsutil samtobam - extra-long-header.bam
+
+
+ ##################################################################
+--- bedtools.orig/test/bamtofastq/test-bamtofastq.sh
++++ bedtools/test/bamtofastq/test-bamtofastq.sh
+@@ -13,7 +13,7 @@
+ fi
+ }
+
+-samtools view -Sb test2.sam > test2.bam 2> /dev/null
++../htsutil samtobam test2.sam test2.bam
+
+ $BT bamtofastq -i test2.bam -fq test2.fq -fq2 test2.fq2 2> /dev/null
+
+--- bedtools.orig/test/bedtobam/test-bedtobam.sh
++++ bedtools/test/bedtobam/test-bedtobam.sh
+@@ -19,7 +19,7 @@
+ echo -e " bedtobam.t1...\c"
+ echo \
+ "read_name 0 1 1001 255 1000M * 0 0 * *">exp
+-echo -e "1\t1000\t2000\tread_name\t255\t+" | $BT bedtobam -i - -g chrsize.tmp| samtools view > obs
++echo -e "1\t1000\t2000\tread_name\t255\t+" | $BT bedtobam -i - -g chrsize.tmp| ../htsutil viewbamrecords > obs
+ check obs exp
+ rm obs exp
+
+--- bedtools.orig/test/coverage/test-coverage.sh
++++ bedtools/test/coverage/test-coverage.sh
+@@ -18,11 +18,10 @@
+ # BAM files #
+ ###########################################################
+ ###########################################################
+-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
+-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
+-samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null
+-samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null
+-
++../htsutil samtobam one_block.sam one_block.bam
++../htsutil samtobam two_blocks.sam two_blocks.bam
++../htsutil samtobam three_blocks.sam three_blocks.bam
++../htsutil samtobam sam-w-del.sam sam-w-del.bam
+
+
+ ##################################################################
+@@ -731,4 +730,6 @@
+ check exp obs
+ rm exp obs
+
++rm one_block.bam two_blocks.bam three_blocks.bam sam-w-del.bam
++
+ [[ $FAILURES -eq 0 ]] || exit 1;
+--- bedtools.orig/test/genomecov/test-genomecov.sh
++++ bedtools/test/genomecov/test-genomecov.sh
+@@ -18,13 +18,14 @@
+ # BAM files #
+ ###########################################################
+ ###########################################################
+-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
+-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
+-samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null
+-samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null
+-samtools view -Sb pair-chip.sam > pair-chip.bam 2>/dev/null
+-samtools view -Sb chip.sam > chip.bam 2>/dev/null
++../htsutil samtobam one_block.sam one_block.bam
++../htsutil samtobam two_blocks.sam two_blocks.bam
++../htsutil samtobam three_blocks.sam three_blocks.bam
++../htsutil samtobam sam-w-del.sam sam-w-del.bam
++../htsutil samtobam pair-chip.sam pair-chip.bam
++../htsutil samtobam chip.sam chip.bam
+
++(grep '^@' one_block.sam; sed '/^@/d' *block*.sam) | ../htsutil samtobam - merged.bam
+
+
+ ##################################################################
+@@ -76,7 +77,7 @@
+ chr1 30 40 2
+ chr1 40 50 1
+ chr1 50 1000 0" > exp
+-samtools merge -f /dev/stdout *block*.bam | $BT genomecov -ibam - -bga > obs
++cat merged.bam | $BT genomecov -ibam - -bga > obs
+ check obs exp
+ rm obs exp
+
+@@ -93,7 +94,7 @@
+ chr1 25 30 3
+ chr1 30 50 1
+ chr1 50 1000 0" > exp
+-samtools merge -f /dev/stdout *block*.bam | $BT genomecov -ibam - -bga -split > obs
++$BT genomecov -ibam merged.bam -bga -split > obs
+ check obs exp
+ rm obs exp
+
+@@ -260,7 +261,7 @@
+ check obs exp
+ rm obs exp
+
+-rm one_block.bam two_blocks.bam three_blocks.bam sam-w-del.bam pair-chip.bam chip.bam
++rm one_block.bam two_blocks.bam three_blocks.bam sam-w-del.bam pair-chip.bam chip.bam merged.bam
+
+ ##################################################################
+ # Make sure empty bam doesn't cause failure
+--- bedtools.orig/test/intersect/new_test-intersect.sh
++++ bedtools/test/intersect/new_test-intersect.sh
+@@ -14,7 +14,7 @@
+
+ bam_check()
+ {
+- if diff <(samtools view $1) <(samtools view $2)
++ if diff <(../htsutil viewbamrecords $1) <(../htsutil viewbamrecords $2)
+ then
+ echo ok
+ else
+@@ -740,21 +740,12 @@
+ # Test that an empty query with header, bgzipped, that
+ # runs with -header option will print header
+ ############################################################
+-
+-# I'm not quite sure what this test was trying to do.
+-# It may have been attempting to test bzip2 compression,
+-# which bedtools does not currently support, or bgzf compression,
+-# which is exceedingly rare outside of a BAM file. At any rate,
+-# it fails on systems without a "bgzip" command, so I've commented
+-# it out for now. NEK 10/02/2017.
+ echo -e " intersect.new.t61...\c"
+-echo ok
+-#echo "#Random Header" >dummy.txt
+-#bgzip dummy.txt
+-#echo "#Random Header" >exp
+-#$BT intersect -a dummy.txt.gz -b a.bed -header > obs
+-#check obs exp
+-#rm obs dummy.txt.gz exp
++echo "#Random Header" | ../htsutil bgzfcompress - dummy.txt.gz
++echo "#Random Header" >exp
++$BT intersect -a dummy.txt.gz -b a.bed -header > obs
++check obs exp
++rm obs dummy.txt.gz exp
+
+
+ ###########################################################
+@@ -910,7 +901,7 @@
+ echo \
+ "FCC1MK2ACXX:2:2110:4301:28831# 99 chr1 10004 0 100M = 10047 140 * * PG:Z:novoalign AM:i:2 SM:i:2 MQ:i:0 PQ:i:219 UQ:i:0 AS:i:0 RG:Z:NCH411GBM_CD133low
+ FCC1MK2ACXX:2:2110:4301:28831# 147 chr1 10047 0 3S97M = 10004 -140 * * PG:Z:novoalign AM:i:2 SM:i:70 MQ:i:0 PQ:i:219 UQ:i:194 AS:i:194 RG:Z:NCH411GBM_CD133low" > exp
+-$BT intersect -a a.cram -b b.cram | samtools view - > obs
++$BT intersect -a a.cram -b b.cram | ../htsutil viewbamrecords > obs
+ check exp obs
+ rm exp obs
+ [[ $FAILURES -eq 0 ]] || exit 1;
+@@ -936,7 +927,7 @@
+ echo \
+ "FCC1MK2ACXX:2:2110:4301:28831# 99 chr1 10004 0 100M = 10047 140 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT CCCFFFFFHHHHHJJIJJJJIGIIIJIGIGJJJJIJJJJIJIIJJDIIIJJIJEHEE at GAHHGE@CEFB;A>AB=??5?B?2?<ABDAD9ABBBC9ABDA PG:Z:novoalign AM:i:2 SM:i:2 MQ:i:0 PQ:i:219 UQ:i:0 AS:i:0 MD:Z:100 NM:i:0 RG:Z:NCH411GBM_CD133low
+ FCC1MK2ACXX:2:2110:4301:28831# 147 chr1 10047 0 3S97M = 10004 -140 AACCCTACCCCTACCCCTAACCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCC ###?<55-@?250&A?882(@?795&B?8;;/?8('9'A?;8?8C;(<A at FB-/7'F?((@0D:)*9JIIHFCJJJIHFJJJIHEJJHHFFHFFFDDCCB PG:Z:novoalign AM:i:2 SM:i:70 MQ:i:0 PQ:i:219 UQ:i:194 AS:i:194 MD:Z:4A5A11A5A5A5A5A5A5A3A34 NM:i:10 RG:Z:NCH411GBM_CD133low">exp
+-CRAM_REFERENCE=test_ref.fa $BT intersect -a a.cram -b b.cram | samtools view -T test_ref.fa - > obs
++CRAM_REFERENCE=test_ref.fa $BT intersect -a a.cram -b b.cram | ../htsutil viewcramrecords - test_ref.fa > obs
+ check exp obs
+ rm exp obs
+ [[ $FAILURES -eq 0 ]] || exit 1;
+@@ -954,7 +945,7 @@
+ GA5:3:49:1480:1116#0 16 dummy_chr 11913868 37 76M * 0 0 GGGAGGAGGCCAGGACTTCAGGGACCCACAGCCATCACCTCCCTCCCCTGCCCCCTACACACCAACTCTCTGGAAA #################################44:4=944==;=???>=?>==??=A=A;ABA?A?AABAAABBB XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75
+ GA5:3:61:213:1812#0 16 dummy_chr 13030396 37 76M * 0 0 GGTCCGGCGGGGTCGGACTGGACCAGCTGTTGGGCTTTGTTTGCTCTTTTTACGAATTGAAAAACTGAAGCCAGGA /=81,5948=485=4,),1;;7:87:6=;;@@AB=C8A@@BAB=>5>BBBB>BBAAA9ABA at B4B;BBBBBBBBCB XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75
+ GA5:3:116:1581:552#0 16 dummy_chr 15055984 37 76M * 0 0 AGAAAGCCTAAGGTCAGGGTGCCAGCAGGTTTGGTGTCTGGTGAGGTACCCATCTCTGCTTCTAAGGCAGAGCCTT 48887429,3=;98<8<8@;<=?8@??98@@@<=AA>@@?B?A@@BA6BA@=@BABBB???B at BBBBBABBCBB?B XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76" > exp
+-$BT intersect -a notexthdr.bam -b notexthdr.bam | samtools view > obs
++$BT intersect -a notexthdr.bam -b notexthdr.bam | ../htsutil viewbamrecords > obs
+ check exp obs
+ rm exp obs
+ [[ $FAILURES -eq 0 ]] || exit 1;
+@@ -976,7 +967,7 @@
+ ############################################################
+ echo -e " intersect.new.t78...\c"
+ echo -e "@HD VN:1.5 SO:coordinate" > exp
+-echo "@HD VN:1.5 SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs
++echo "@HD VN:1.5 SO:coordinate" | ../htsutil samtobam - - | $BT intersect -a /dev/stdin -b b.bed | ../htsutil viewbam >obs
+ check exp obs
+ rm exp obs
+ [[ $FAILURES -eq 0 ]] || exit 1;
+--- bedtools.orig/test/intersect/performanceTest.sh
++++ bedtools/test/intersect/performanceTest.sh
+@@ -27,8 +27,7 @@
+ ../$BT random -l 1000 -n 10000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > b10M.bed
+ cp a10M.bed a10M_gzipped.bed
+ gzip a10M_gzipped.bed
+- cp a10M.bed a10M_bgzipped.bed
+- bgzip a10M_bgzipped.bed
++ ../../htsutil bgzfcompress a10M.bed a10M_bgzipped.bed.gz
+ ../$BT bedtobam -i a10M.bed -g ../human.hg19.genome > a10M.bam
+ cd ..
+ fi
+--- bedtools.orig/test/intersect/test-intersect.sh
++++ bedtools/test/intersect/test-intersect.sh
+@@ -196,10 +196,10 @@
+ # -split #
+ ###########################################################
+ ###########################################################
+-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
+-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
+-samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null
+-samtools view -Sb split.issue750.sam > split.issue750.bam 2>/dev/null
++../htsutil samtobam one_block.sam one_block.bam
++../htsutil samtobam two_blocks.sam two_blocks.bam
++../htsutil samtobam three_blocks.sam three_blocks.bam
++../htsutil samtobam split.issue750.sam split.issue750.bam
+
+
+ ##################################################################
+@@ -208,7 +208,7 @@
+ echo -e " intersect.t17...\c"
+ echo \
+ "three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp
+-$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed | samtools view - > obs
++$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed | ../htsutil viewbamrecords > obs
+ check obs exp
+ rm obs exp
+
+@@ -217,7 +217,7 @@
+ ##################################################################
+ echo -e " intersect.t18...\c"
+ touch exp
+-$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed -split | samtools view - > obs
++$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed -split | ../htsutil viewbamrecords > obs
+ check obs exp
+ rm obs exp
+
+@@ -227,7 +227,7 @@
+ echo -e " intersect.t19...\c"
+ echo \
+ "three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp
+-$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split | samtools view - > obs
++$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split | ../htsutil viewbamrecords > obs
+ check obs exp
+ rm obs exp
+
+@@ -237,7 +237,7 @@
+ ##################################################################
+ echo -e " intersect.t20...\c"
+ touch exp
+-$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split -s | samtools view - > obs
++$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split -s | ../htsutil viewbamrecords > obs
+ check obs exp
+ rm obs exp
+
+@@ -247,7 +247,7 @@
+ echo -e " intersect.t21...\c"
+ echo \
+ "three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp
+-$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split | samtools view - > obs
++$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split | ../htsutil viewbamrecords > obs
+ check obs exp
+ rm obs exp
+
+@@ -256,7 +256,7 @@
+ ################################################################################
+ echo -e " intersect.t22...\c"
+ touch exp
+-$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split -f 0.1 | samtools view - > obs
++$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split -f 0.1 | ../htsutil viewbamrecords > obs
+ check obs exp
+ rm obs exp
+
+@@ -590,7 +590,7 @@
+ echo -e " intersect.t23...\c"
+ echo \
+ "mapped 16 chr1 1 40 30M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp
+-samtools view -Sb mapped_and_unmapped.sam 2>/dev/null | $BT intersect -abam - -b a.bed | samtools view - > obs
++../htsutil samtobam mapped_and_unmapped.sam | $BT intersect -abam - -b a.bed | ../htsutil viewbamrecords > obs
+ check obs exp
+ rm obs exp
+
+@@ -600,7 +600,7 @@
+ echo -e " intersect.t24...\c"
+ echo \
+ "umapped 4 * 1 40 30M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp
+-samtools view -Sb mapped_and_unmapped.sam 2>/dev/null | $BT intersect -abam - -b a.bed -v | samtools view - > obs
++../htsutil samtobam mapped_and_unmapped.sam | $BT intersect -abam - -b a.bed -v | ../htsutil viewbamrecords > obs
+ check obs exp
+ rm obs exp
+
+@@ -977,34 +977,34 @@
+ ##################################################################
+ echo -e " intersect.t63...\c"
+ echo -n "" > exp
+-$BT intersect -a x.bam -b y.bed -f 0.21 -F 0.21 -wa | samtools view - > obs
++$BT intersect -a x.bam -b y.bed -f 0.21 -F 0.21 -wa | ../htsutil viewbamrecords > obs
+ check exp obs
+ rm exp obs
+
+ echo -e " intersect.t64...\c"
+ echo "a1 0 chr1 11 255 10M * 0 0 * *
+ a2 16 chr2 11 255 10M * 0 0 * *" > exp
+-$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.21 -wa | samtools view - > obs
++$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.21 -wa | ../htsutil viewbamrecords > obs
+ check exp obs
+ rm exp obs
+
+ echo -e " intersect.t65...\c"
+ echo "a1 0 chr1 11 255 10M * 0 0 * *
+ a2 16 chr2 11 255 10M * 0 0 * *" > exp
+-$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.21 -wa | samtools view - > obs
++$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.21 -wa | ../htsutil viewbamrecords > obs
+ check exp obs
+ rm exp obs
+
+ echo -e " intersect.t66...\c"
+ echo "a1 0 chr1 11 255 10M * 0 0 * *
+ a2 16 chr2 11 255 10M * 0 0 * *" > exp
+-$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.50 -wa | samtools view - > obs
++$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.50 -wa | ../htsutil viewbamrecords > obs
+ check exp obs
+ rm exp obs
+
+ echo -e " intersect.t67...\c"
+ echo -n "" > exp
+-$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.51 -wa | samtools view - > obs
++$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.51 -wa | ../htsutil viewbamrecords > obs
+ check exp obs
+ rm exp obs
+
+--- bedtools.orig/test/multicov/test-multicov.sh
++++ bedtools/test/multicov/test-multicov.sh
+@@ -13,14 +13,10 @@
+ fi
+ }
+
+-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
+-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
+-samtools view -Sb test-multi.sam > test-multi.bam 2>/dev/null
+-samtools view -Sb test-multi.2.sam > test-multi.2.bam 2>/dev/null
+-samtools index one_block.bam
+-samtools index two_blocks.bam
+-samtools index test-multi.bam
+-samtools index test-multi.2.bam
++../htsutil samtoindexedbam one_block.sam one_block.bam
++../htsutil samtoindexedbam two_blocks.sam two_blocks.bam
++../htsutil samtoindexedbam test-multi.sam test-multi.bam
++../htsutil samtoindexedbam test-multi.2.sam test-multi.2.bam
+
+ ##################################################################
+ # Test one block matches all BEDs
=====================================
debian/patches/series
=====================================
@@ -9,3 +9,4 @@ remove_barski_binding_site.png.patch
fix_intersect_test.patch
spelling
hardening
+no-samtools
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, samtools, tabix
+Depends: @, tabix
Restrictions: allow-stderr
View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/commit/fdd468037455494cf27f2f0b6b8cdecb6f31441c
--
View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/commit/fdd468037455494cf27f2f0b6b8cdecb6f31441c
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