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Update submodules to work with GCC 10 #67

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Update submodules to work with GCC 10 #67

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b714d5d
Get rid of all submodules
julianhess Dec 15, 2022
8ad09a7
Add updated fermi-lite submodule
julianhess Dec 15, 2022
a26830b
Update BWA submodule
julianhess Dec 15, 2022
f9c934e
Update fermi-lite submodule again
julianhess Dec 15, 2022
fc6b806
Use https for submodules, so that SSH keys aren't required to clone
julianhess Jan 23, 2024
0a54514
Bump bwa/fermi submodules
julianhess Aug 9, 2024
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7 changes: 2 additions & 5 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,9 +1,6 @@
[submodule "fermi-lite"]
path = fermi-lite
url = https://github.com/walaj/fermi-lite
[submodule "htslib"]
path = htslib
url = https://github.com/samtools/htslib
url = https://github.com/julianhess/fermi-lite.git
[submodule "bwa"]
path = bwa
url = https://github.com/walaj/bwa
url = https://github.com/lh3/bwa.git
2 changes: 1 addition & 1 deletion bwa
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Submodule bwa updated 39 files
+46 −0 .github/workflows/ci.yaml
+0 −5 .travis.yml
+5 −5 Makefile
+29 −1 NEWS.md
+27 −15 README.md
+13 −8 bntseq.c
+3 −3 bntseq.h
+52 −6 bwa.1
+60 −9 bwa.c
+29 −1 bwa.h
+1 −1 bwakit/bwa-postalt.js
+4 −3 bwakit/run-bwamem
+1 −1 bwakit/run-gen-ref
+48 −10 bwamem.c
+28 −0 bwamem.h
+33 −2 bwamem_extra.c
+26 −0 bwamem_pair.c
+3 −2 bwape.c
+6 −3 bwase.c
+4 −2 bwt.h
+1,629 −0 bwt_gen.c
+1 −1 bwt_lite.c
+3 −2 bwtaln.c
+1 −1 bwtgap.c
+3 −3 bwtgap.h
+5 −6 bwtindex.c
+2 −2 bwtsw2_core.c
+7 −1 bwtsw2_pair.c
+30 −0 code_of_conduct.md
+46 −6 fastmap.c
+41 −5 ksw.c
+1 −0 kthread.c
+29 −3 main.c
+4 −4 malloc_wrap.c
+33 −0 neon_sse.h
+1 −1 rle.h
+119 −0 scalar_sse.h
+16 −5 utils.c
+6 −6 utils.h
2 changes: 1 addition & 1 deletion fermi-lite
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Submodule fermi-lite updated 15 files
+2 −2 Makefile
+9 −2 README.md
+1 −1 bfc.c
+2 −2 bseq.c
+6 −7 bubble.c
+7 −2 example.c
+48 −11 f_ksw.c
+6 −3 fml.h
+5 −4 mag.c
+1 −1 mag.h
+9 −4 misc.c
+33 −0 neon_sse.h
+1 −1 rle.h
+119 −0 scalar_sse.h
+2 −2 unitig.c