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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/bedtools">Debian Med / bedtools</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/bedtools/-/commit/fdd468037455494cf27f2f0b6b8cdecb6f31441c">fdd46803</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-02-14T16:53:00+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove the need for samtools via patch from upstream.
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#c01a5549a47d3878d06fe57012e999b00bc461bb">
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+
debian/patches/no-samtools
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bedtools/-/commit/fdd468037455494cf27f2f0b6b8cdecb6f31441c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bedtools (2.29.2+dfsg-4) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Remove the need for samtools via patch from upstream.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 14 Feb 2020 16:50:58 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">bedtools (2.29.2+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bedtools/-/commit/fdd468037455494cf27f2f0b6b8cdecb6f31441c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,8 +8,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libbz2-dev,</span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> liblzma-dev,</span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> samtools (>= 1.10)</span>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> liblzma-dev</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bedtools</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bedtools.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +18,6 @@ Package: bedtools</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Recommends: samtools (>= 1.10)</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Conflicts: filo</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Provides: filo</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Replaces: filo</span>
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<li id="c01a5549a47d3878d06fe57012e999b00bc461bb">
<a href="https://salsa.debian.org/med-team/bedtools/-/commit/fdd468037455494cf27f2f0b6b8cdecb6f31441c#c01a5549a47d3878d06fe57012e999b00bc461bb"><strong>debian/patches/no-samtools</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: John Marshall <John.W.Marshall@glasgow.ac.uk></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Date: Tue, 16 Apr 2019 11:48:55 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Subject: Use new htsutil.cpp in test suite instead of samtools</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: https://github.com/arq5x/bedtools2/pull/818</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/.github/workflows/main.yml</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/.github/workflows/main.yml</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -9,8 +9,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> steps:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> - uses: actions/checkout@v1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- - name: Install samtools</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run: sudo apt-get install -y samtools </span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> - name: Compile and test Bedtools</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> run: make -j8 && make test</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> - name: Compile static binary</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/.gitignore</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/.gitignore</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -12,12 +12,16 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> .cproject</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> nbproject</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> sandbox</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+test/coverage/*.bam</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+test/coverage/*.bam.bai</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> test/general/o</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> test/genomecov/chip.bam</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+test/genomecov/merged.bam</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> test/genomecov/one_block.bam</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> test/genomecov/pair-chip.bam</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> test/genomecov/sam-w-del.bam</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> test/genomecov/three_blocks.bam</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+test/htsutil</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> test/multicov/one_block.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> test/multicov/two_blocks.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> test/genomecov/two_blocks.bam</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -130,7 +130,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> ALL_LIBS = $(BT_LIBS) $(LIBS)</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all: print_banner $(BIN_DIR)/bedtools $(BIN_DIR)/intersectBed</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all: print_banner $(BIN_DIR)/bedtools $(BIN_DIR)/intersectBed test/htsutil</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> static: print_banner $(BIN_DIR)/bedtools.static</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -163,6 +163,9 @@</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> $(OBJ_DIR)/bedtools.o: $(SRC_DIR)/bedtools.cpp $(OBJ_DIR)/bedtools.d</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> $(CXX_COMPILE)</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$(OBJ_DIR)/htsutil.o: $(SRC_DIR)/htsutil.cpp $(OBJ_DIR)/htsutil.d</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX_COMPILE)</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> # HTSlib's htslib.mk provides rules to rebuild $(HTSDIR)/libhts.a.</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> HTSDIR = src/utils/htslib</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> include $(HTSDIR)/htslib.mk</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="p">@@ -181,6 +184,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> $(CCPREFIX) $(CC_WRAPPER) $(CXX) -static $(ALL_LDFLAGS) -o $(BIN_DIR)/bedtools.static $(BUILT_OBJECTS) $(HTSDIR)/libhts.a $(ALL_LIBS)</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> @echo "done."</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+test/htsutil: $(OBJ_DIR)/htsutil.o $(HTSDIR)/libhts.a</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_LDFLAGS) -o test/htsutil $(OBJ_DIR)/htsutil.o $(HTSDIR)/libhts.a $(ALL_LIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> $(BIN_DIR)/intersectBed: | $(BIN_DIR)</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> @echo "- Creating executables for old CLI."</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> @python3 scripts/makeBashScripts.py</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -211,7 +217,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> # not existing), so clean should also remove the generated config.h.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> @echo " * Cleaning up."</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @rm -f $(VERSION_FILE) $(OBJ_DIR)/* $(BIN_DIR)/*</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @rm -f $(VERSION_FILE) $(OBJ_DIR)/* $(BIN_DIR)/* test/htsutil</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> @cd src/utils/htslib && make clean > /dev/null</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> @test -e src/utils/htslib/config.mk || rm -f src/utils/htslib/config.h</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> .PHONY: clean</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/src/htsutil.cpp</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -0,0 +1,167 @@</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <fstream></span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <iostream></span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <string></span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <htslib/bgzf.h></span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <htslib/sam.h></span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+int convert(htsExactFormat outformat, const char *outfname, bool outheaders,</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ htsExactFormat informat, const char *infname,</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const char *reffname = NULL)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ htsFile* in = NULL;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ htsFile* out = NULL;</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bam_hdr_t* hdr = NULL;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bam1_t* b = NULL;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ in = hts_open(infname, "r");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (in == NULL)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw std::string("can't open ") + infname;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (hts_get_format(in)->format != informat)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw std::string(infname) + ": file is in the wrong format";</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const char *outf = "w";</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ switch (outformat) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case sam: outf = "w"; break;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case bam: outf = "wb"; break;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case cram: outf = "wc"; break;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ default: throw std::string("invalid outformat argument");</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ out = hts_open(outfname, outf);</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (out == NULL)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw std::string("can't write to ") + outfname;</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (reffname) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hts_set_fai_filename(in, reffname);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hts_set_fai_filename(out, reffname);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hdr = sam_hdr_read(in);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (hdr == NULL)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw std::string("can't read headers from ") + infname;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (outheaders) {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (sam_hdr_write(out, hdr) < 0)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw std::string("can't write headers to ") + outfname;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int ret;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ b = bam_init1();</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while ((ret = sam_read1(in, hdr, b)) >= 0) {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (sam_write1(out, hdr, b) < 0)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw std::string("can't write record to ") + outfname;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (ret < -1)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw std::string("truncated input file");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bam_destroy1(b);</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
</td>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bam_hdr_destroy(hdr);</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hts_close(out);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hts_close(in);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ catch (const std::string& what) {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cerr << "htsutil: " << what << '\n';</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bam_destroy1(b);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bam_hdr_destroy(hdr);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (out) hts_close(out);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (in) hts_close(in);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 0;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+int compress(const char *outfname, std::streambuf* in)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ BGZF* out = NULL;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ out = bgzf_open(outfname, "w");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (out == NULL)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw std::string("can't write to ") + outfname;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char buffer[65536];</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ size_t n;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while ((n = in->sgetn(buffer, sizeof buffer)) > 0) {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (bgzf_write(out, buffer, n) < 0)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw std::string("can't write to ") + outfname;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bgzf_close(out);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ catch (const std::string& what) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cerr << "htsutil: " << what << '\n';</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (out) bgzf_close(out);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 0;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+int compress(const char *outfname, const char *infname)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (std::string(infname) == "-")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return compress(outfname, std::cin.rdbuf());</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::filebuf in;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (in.open(infname, std::ios::in) == NULL) {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cerr << "htsutil: can't open " << infname << '\n';</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return compress(outfname, &in);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+int index(const char *fname, bool csi)</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (std::string(fname) == "-") {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cerr << "htsutil: can't index standard output\n";</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1;</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int ret = sam_index_build(fname, csi? 14 : 0);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (ret < 0) return -ret; // Convert to exit status</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 0;</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+int main(int argc, char **argv)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::string cmd = (argc >= 2)? argv[1] : "--help";</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const char *src = (argc >= 3)? argv[2] : "-";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const char *dest= (argc >= 4)? argv[3] : "-";</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd == "viewbamrecords")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return convert(sam, "-", false, bam, src);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else if (cmd == "viewbam")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return convert(sam, "-", true, bam, src);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else if (cmd == "viewcramrecords")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return convert(sam, "-", false, cram, src, (argc >= 4)? argv[3] : NULL);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else if (cmd == "bgzfcompress")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return compress(dest, src);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else if (cmd == "index")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return index(src, false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else if (cmd == "indexcsi")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return index(src, true);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else if (cmd == "samtobam")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return convert(bam, dest, true, sam, src);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else if (cmd == "samtoindexedbam") {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int ret = convert(bam, dest, true, sam, src);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (ret != 0) return ret;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return index(dest, false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
233
</td>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cerr <<</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+"Usage: htsutil bgzfcompress [SRCFILE [DESTFILE]]\n"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
235
</td>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" htsutil index FILE\n"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
236
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" htsutil indexcsi FILE\n"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" htsutil samtobam [SRCFILE [DESTFILE]]\n"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" htsutil samtoindexedbam SRCFILE DESTFILE\n"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" htsutil viewbam [FILE]\n"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" htsutil viewbamrecords [FILE]\n"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" htsutil viewcramrecords [FILE [REFFILE]]\n";</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1;</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/bamtobed/test-bamtobed.sh</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/bamtobed/test-bamtobed.sh</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="p">@@ -18,13 +18,13 @@</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> # BAM files #</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> ###########################################################</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> ###########################################################</span>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb two_blocks_w_D.sam > two_blocks_w_D.bam 2>/dev/null</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb numeric_tag.sam > numeric_tag.bam 2> /dev/null</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-gzip -dfc extra-long-header.sam | samtools view -Sb > extra-long-header.bam 2> /dev/null</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam one_block.sam one_block.bam</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam two_blocks.sam two_blocks.bam</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam three_blocks.sam three_blocks.bam</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#../htsutil samtobam sam-w-del.sam sam-w-del.bam</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam two_blocks_w_D.sam two_blocks_w_D.bam</span></span>
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<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam numeric_tag.sam numeric_tag.bam</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+gzip -dfc extra-long-header.sam | ../htsutil samtobam - extra-long-header.bam</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> </span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> </span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> ##################################################################</span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/bamtofastq/test-bamtofastq.sh</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/bamtofastq/test-bamtofastq.sh</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> fi</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> }</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb test2.sam > test2.bam 2> /dev/null</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam test2.sam test2.bam</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> </span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> $BT bamtofastq -i test2.bam -fq test2.fq -fq2 test2.fq2 2> /dev/null</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/bedtobam/test-bedtobam.sh</span></span>
</pre>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/bedtobam/test-bedtobam.sh</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> echo -e " bedtobam.t1...\c"</span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> echo \</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> "read_name 0 1 1001 255 1000M * 0 0 * *">exp</span>
</pre>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-echo -e "1\t1000\t2000\tread_name\t255\t+" | $BT bedtobam -i - -g chrsize.tmp| samtools view > obs</span></span>
</pre>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo -e "1\t1000\t2000\tread_name\t255\t+" | $BT bedtobam -i - -g chrsize.tmp| ../htsutil viewbamrecords > obs</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> check obs exp</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> rm obs exp</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> </span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/coverage/test-coverage.sh</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/coverage/test-coverage.sh</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="p">@@ -18,11 +18,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> # BAM files #</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> ###########################################################</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> ###########################################################</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam one_block.sam one_block.bam</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam two_blocks.sam two_blocks.bam</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam three_blocks.sam three_blocks.bam</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam sam-w-del.sam sam-w-del.bam</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> ##################################################################</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="p">@@ -731,4 +730,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> check exp obs</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> rm exp obs</span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rm one_block.bam two_blocks.bam three_blocks.bam sam-w-del.bam</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> [[ $FAILURES -eq 0 ]] || exit 1;</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/genomecov/test-genomecov.sh</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/genomecov/test-genomecov.sh</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="p">@@ -18,13 +18,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> # BAM files #</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> ###########################################################</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> ###########################################################</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb pair-chip.sam > pair-chip.bam 2>/dev/null</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb chip.sam > chip.bam 2>/dev/null</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam one_block.sam one_block.bam</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam two_blocks.sam two_blocks.bam</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam three_blocks.sam three_blocks.bam</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam sam-w-del.sam sam-w-del.bam</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam pair-chip.sam pair-chip.bam</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam chip.sam chip.bam</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+(grep '^@' one_block.sam; sed '/^@/d' *block*.sam) | ../htsutil samtobam - merged.bam</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> ##################################################################</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="p">@@ -76,7 +77,7 @@</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> chr1 30 40 2</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> chr1 40 50 1</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> chr1 50 1000 0" > exp</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools merge -f /dev/stdout *block*.bam | $BT genomecov -ibam - -bga > obs</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+cat merged.bam | $BT genomecov -ibam - -bga > obs</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> check obs exp</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> rm obs exp</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> </span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="p">@@ -93,7 +94,7 @@</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> chr1 25 30 3</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> chr1 30 50 1</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> chr1 50 1000 0" > exp</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools merge -f /dev/stdout *block*.bam | $BT genomecov -ibam - -bga -split > obs</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT genomecov -ibam merged.bam -bga -split > obs</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> check obs exp</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> rm obs exp</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="p">@@ -260,7 +261,7 @@</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> check obs exp</span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> rm obs exp</span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-rm one_block.bam two_blocks.bam three_blocks.bam sam-w-del.bam pair-chip.bam chip.bam</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rm one_block.bam two_blocks.bam three_blocks.bam sam-w-del.bam pair-chip.bam chip.bam merged.bam</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> ##################################################################</span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> # Make sure empty bam doesn't cause failure</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/intersect/new_test-intersect.sh</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/intersect/new_test-intersect.sh</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="p">@@ -14,7 +14,7 @@</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> </span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> bam_check() </span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> {</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if diff <(samtools view $1) <(samtools view $2) </span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if diff <(../htsutil viewbamrecords $1) <(../htsutil viewbamrecords $2)</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> then</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> echo ok</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> else</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="p">@@ -740,21 +740,12 @@</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> # Test that an empty query with header, bgzipped, that</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> # runs with -header option will print header</span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> ############################################################</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# I'm not quite sure what this test was trying to do.</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# It may have been attempting to test bzip2 compression,</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# which bedtools does not currently support, or bgzf compression,</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# which is exceedingly rare outside of a BAM file. At any rate,</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# it fails on systems without a "bgzip" command, so I've commented</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# it out for now. NEK 10/02/2017.</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> echo -e " intersect.new.t61...\c"</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-echo ok</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#echo "#Random Header" >dummy.txt</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#bgzip dummy.txt</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#echo "#Random Header" >exp</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#$BT intersect -a dummy.txt.gz -b a.bed -header > obs</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#check obs exp</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#rm obs dummy.txt.gz exp</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "#Random Header" | ../htsutil bgzfcompress - dummy.txt.gz</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "#Random Header" >exp</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -a dummy.txt.gz -b a.bed -header > obs</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+check obs exp</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rm obs dummy.txt.gz exp</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> </span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> </span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> ###########################################################</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="p">@@ -910,7 +901,7 @@</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> echo \</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> "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</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> 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</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -a a.cram -b b.cram | samtools view - > obs</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -a a.cram -b b.cram | ../htsutil viewbamrecords > obs</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> check exp obs</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> rm exp obs</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> [[ $FAILURES -eq 0 ]] || exit 1;</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="p">@@ -936,7 +927,7 @@</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> echo \</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> "FCC1MK2ACXX:2:2110:4301:28831# 99 chr1 10004 0 100M = 10047 140 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT CCCFFFFFHHHHHJJIJJJJIGIIIJIGIGJJJJIJJJJIJIIJJDIIIJJIJEHEE@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</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> 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@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</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CRAM_REFERENCE=test_ref.fa $BT intersect -a a.cram -b b.cram | samtools view -T test_ref.fa - > obs</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CRAM_REFERENCE=test_ref.fa $BT intersect -a a.cram -b b.cram | ../htsutil viewcramrecords - test_ref.fa > obs</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> check exp obs</span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> rm exp obs</span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> [[ $FAILURES -eq 0 ]] || exit 1;</span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="p">@@ -954,7 +945,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> GA5:3:49:1480:1116#0 16 dummy_chr 11913868 37 76M * 0 0 GGGAGGAGGCCAGGACTTCAGGGACCCACAGCCATCACCTCCCTCCCCTGCCCCCTACACACCAACTCTCTGGAAA #################################44:4=944==;=???>=?>==??=A=A;ABA?A?AABAAABBB XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> GA5:3:61:213:1812#0 16 dummy_chr 13030396 37 76M * 0 0 GGTCCGGCGGGGTCGGACTGGACCAGCTGTTGGGCTTTGTTTGCTCTTTTTACGAATTGAAAAACTGAAGCCAGGA /=81,5948=485=4,),1;;7:87:6=;;@@AB=C8A@@BAB=>5>BBBB>BBAAA9ABA@B4B;BBBBBBBBCB XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> GA5:3:116:1581:552#0 16 dummy_chr 15055984 37 76M * 0 0 AGAAAGCCTAAGGTCAGGGTGCCAGCAGGTTTGGTGTCTGGTGAGGTACCCATCTCTGCTTCTAAGGCAGAGCCTT 48887429,3=;98<8<8@;<=?8@??98@@@<=AA>@@?B?A@@BA6BA@=@BABBB???B@BBBBBABBCBB?B XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76" > exp</span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -a notexthdr.bam -b notexthdr.bam | samtools view > obs</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -a notexthdr.bam -b notexthdr.bam | ../htsutil viewbamrecords > obs</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"> check exp obs</span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> rm exp obs</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> [[ $FAILURES -eq 0 ]] || exit 1;</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="p">@@ -976,7 +967,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> ############################################################</span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> echo -e " intersect.new.t78...\c"</span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"> echo -e "@HD VN:1.5 SO:coordinate" > exp</span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-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</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "@HD VN:1.5 SO:coordinate" | ../htsutil samtobam - - | $BT intersect -a /dev/stdin -b b.bed | ../htsutil viewbam >obs</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> check exp obs</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> rm exp obs</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> [[ $FAILURES -eq 0 ]] || exit 1;</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/intersect/performanceTest.sh</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/intersect/performanceTest.sh</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="p">@@ -27,8 +27,7 @@</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> ../$BT random -l 1000 -n 10000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > b10M.bed </span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> cp a10M.bed a10M_gzipped.bed</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> gzip a10M_gzipped.bed</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp a10M.bed a10M_bgzipped.bed</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bgzip a10M_bgzipped.bed</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../../htsutil bgzfcompress a10M.bed a10M_bgzipped.bed.gz</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> ../$BT bedtobam -i a10M.bed -g ../human.hg19.genome > a10M.bam</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> cd ..</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"> fi</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/intersect/test-intersect.sh</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/intersect/test-intersect.sh</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"><span class="p">@@ -196,10 +196,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> # -split #</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"> ###########################################################</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> ###########################################################</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb split.issue750.sam > split.issue750.bam 2>/dev/null</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam one_block.sam one_block.bam</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam two_blocks.sam two_blocks.bam</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam three_blocks.sam three_blocks.bam</span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam split.issue750.sam split.issue750.bam</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"> </span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> </span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> ##################################################################</span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="p">@@ -208,7 +208,7 @@</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> echo -e " intersect.t17...\c"</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> echo \</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> "three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp</span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed | samtools view - > obs</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed | ../htsutil viewbamrecords > obs</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> check obs exp</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> rm obs exp</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> </span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="p">@@ -217,7 +217,7 @@</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"> ##################################################################</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"> echo -e " intersect.t18...\c"</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"> touch exp</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed -split | samtools view - > obs</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed -split | ../htsutil viewbamrecords > obs</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> check obs exp</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> rm obs exp</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> </span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="p">@@ -227,7 +227,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"> echo -e " intersect.t19...\c"</span>
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<td class="diff-line-num new new_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> echo \</span>
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<td class="diff-line-num new new_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> "three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split | samtools view - > obs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split | ../htsutil viewbamrecords > obs</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> check obs exp</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> rm obs exp</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> </span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="p">@@ -237,7 +237,7 @@</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"> ##################################################################</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> echo -e " intersect.t20...\c"</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> touch exp</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split -s | samtools view - > obs</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split -s | ../htsutil viewbamrecords > obs</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"> check obs exp</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> rm obs exp</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> </span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"><span class="p">@@ -247,7 +247,7 @@</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> echo -e " intersect.t21...\c"</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> echo \</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> "three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp</span>
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<td class="diff-line-num new new_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split | samtools view - > obs</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split | ../htsutil viewbamrecords > obs</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> check obs exp</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"> rm obs exp</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"> </span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="p">@@ -256,7 +256,7 @@</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"> ################################################################################</span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> echo -e " intersect.t22...\c"</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"> touch exp</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split -f 0.1 | samtools view - > obs</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split -f 0.1 | ../htsutil viewbamrecords > obs</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> check obs exp</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"> rm obs exp</span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> </span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="p">@@ -590,7 +590,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> echo -e " intersect.t23...\c"</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> echo \</span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"> "mapped 16 chr1 1 40 30M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb mapped_and_unmapped.sam 2>/dev/null | $BT intersect -abam - -b a.bed | samtools view - > obs</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam mapped_and_unmapped.sam | $BT intersect -abam - -b a.bed | ../htsutil viewbamrecords > obs</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> check obs exp</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> rm obs exp</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> </span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="p">@@ -600,7 +600,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"> echo -e " intersect.t24...\c"</span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> echo \</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> "umapped 4 * 1 40 30M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb mapped_and_unmapped.sam 2>/dev/null | $BT intersect -abam - -b a.bed -v | samtools view - > obs</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtobam mapped_and_unmapped.sam | $BT intersect -abam - -b a.bed -v | ../htsutil viewbamrecords > obs</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> check obs exp</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> rm obs exp</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> </span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="p">@@ -977,34 +977,34 @@</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"> ##################################################################</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> echo -e " intersect.t63...\c"</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> echo -n "" > exp</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -a x.bam -b y.bed -f 0.21 -F 0.21 -wa | samtools view - > obs</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -a x.bam -b y.bed -f 0.21 -F 0.21 -wa | ../htsutil viewbamrecords > obs</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> check exp obs</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> rm exp obs</span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"> echo -e " intersect.t64...\c"</span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"> echo "a1 0 chr1 11 255 10M * 0 0 * *</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> a2 16 chr2 11 255 10M * 0 0 * *" > exp</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.21 -wa | samtools view - > obs</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.21 -wa | ../htsutil viewbamrecords > obs</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> check exp obs</span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> rm exp obs</span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"> echo -e " intersect.t65...\c"</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"> echo "a1 0 chr1 11 255 10M * 0 0 * *</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> a2 16 chr2 11 255 10M * 0 0 * *" > exp</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.21 -wa | samtools view - > obs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.21 -wa | ../htsutil viewbamrecords > obs</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"> check exp obs</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> rm exp obs</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> </span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> echo -e " intersect.t66...\c"</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> echo "a1 0 chr1 11 255 10M * 0 0 * *</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> a2 16 chr2 11 255 10M * 0 0 * *" > exp</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.50 -wa | samtools view - > obs</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.50 -wa | ../htsutil viewbamrecords > obs</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> check exp obs</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> rm exp obs</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> </span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> echo -e " intersect.t67...\c"</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> echo -n "" > exp</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.51 -wa | samtools view - > obs</span></span>
</pre>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$BT intersect -a x.bam -b y.bed -f 0.19 -F 0.51 -wa | ../htsutil viewbamrecords > obs</span></span>
</pre>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> check exp obs</span>
</pre>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> rm exp obs</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> </span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedtools.orig/test/multicov/test-multicov.sh</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedtools/test/multicov/test-multicov.sh</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="p">@@ -13,14 +13,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb one_block.sam > one_block.bam 2>/dev/null</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb test-multi.sam > test-multi.bam 2>/dev/null</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools view -Sb test-multi.2.sam > test-multi.2.bam 2>/dev/null</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools index one_block.bam</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools index two_blocks.bam</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools index test-multi.bam</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools index test-multi.2.bam</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtoindexedbam one_block.sam one_block.bam</span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtoindexedbam two_blocks.sam two_blocks.bam</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtoindexedbam test-multi.sam test-multi.bam</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+../htsutil samtoindexedbam test-multi.2.sam test-multi.2.bam</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"> </span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> ##################################################################</span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> # Test one block matches all BEDs</span></pre>
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<a href="https://salsa.debian.org/med-team/bedtools/-/commit/fdd468037455494cf27f2f0b6b8cdecb6f31441c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,3 +9,4 @@ remove_barski_binding_site.png.patch</td>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">fix_intersect_test.patch</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">spelling</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">hardening</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">no-samtools</span></pre>
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<a href="https://salsa.debian.org/med-team/bedtools/-/commit/fdd468037455494cf27f2f0b6b8cdecb6f31441c#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @, <span class="idiff left right">samtools, </span>tabix</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, tabix</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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