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update FASTGA and FASTAN to latest commits #1876

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update FASTGA and FASTAN to latest commits #1876

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4eaf357
update FASTGA and FASTAN to latest commits
glennhickey Jan 14, 2026
5a3d0f5
hack fastga build to use pthread
glennhickey Jan 14, 2026
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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -313,7 +313,7 @@ suball.collapse-bubble:
chmod +x submodules/collapse-bubble/scripts/merge_duplicates.py
ln -f submodules/collapse-bubble/scripts/merge_duplicates.py ${BINDIR}
suball.FASTGA:
cd submodules/FASTGA && ${MAKE}
cd submodules/FASTGA && sed -i '/-lpthread/!s/-lm -lz/-lpthread -lm -lz/g' Makefile && ${MAKE}
ln -f submodules/FASTGA/FastGA ${BINDIR}
ln -f submodules/FASTGA/ALNtoPAF ${BINDIR}
ln -f submodules/FASTGA/FAtoGDB ${BINDIR}
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2 changes: 1 addition & 1 deletion submodules/FASTAN
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Submodule FASTAN updated 13 files
+907 −0 ANO.c
+86 −0 ANO.h
+245 −275 FasTAN.c
+784 −0 FastLTR.c
+704 −0 FastMICRO.c
+299 −135 GDB.c
+44 −15 GDB.h
+10 −4 Makefile
+3 −3 ONElib.c
+1,475 −706 align.c
+16 −10 align.h
+0 −185 alncode.c
+0 −3 alncode.h
2 changes: 1 addition & 1 deletion submodules/FASTGA
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Submodule FASTGA updated 31 files
+4 −4 ALNchain.c
+4 −4 ALNplot.c
+7 −6 ALNreset.c
+9 −7 ALNshow.c
+95 −39 ALNtoPAF.c
+5 −3 ALNtoPSL.c
+907 −0 ANO.c
+86 −0 ANO.h
+285 −0 ANOshow.c
+476 −0 ANOstat.c
+152 −0 ANOtoBED.c
+380 −0 BEDtoANO.c
+19 −6 FAtoGDB.c
+52 −22 FastGA.c
+299 −135 GDB.c
+44 −15 GDB.h
+69 −10 GDBshow.c
+3 −20 GDBstat.c
+90 −40 GDBtoFA.c
+58 −20 GIXmake.c
+24 −9 Makefile
+20 −10 ONEaln.c
+45 −38 ONElib.c
+20 −10 ONElib.h
+6 −16 PAFtoALN.c
+168 −75 README.md
+1,475 −706 align.c
+16 −10 align.h
+33 −185 alncode.c
+2 −6 alncode.h
+6 −1 select.c