xmatchview: add example using PAF files

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Sun Jun 20 13:54:23 2021 -0600
Changeset:	14773393ba33108bf7c9551560d1596638d130b6

Modified Files:
	xmatchview/Makefile
	xmatchview/files/Makefile.xmatchview

Log Message:
xmatchview: add example using PAF files

xmatchview can create graphics based upon *.rep files created by
cross_match (part of phrap) and *.paf files created by minimap2.
However, the original example and test only illustrated the former,
even though the relevant files are present to illustrate the latter.
Extend the example to illustrate use of xmatchview to create graphics
from PAF files as well.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=14773393ba33108bf7c9551560d1596638d130b6

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 xmatchview/Makefile                  |  1 +
 xmatchview/files/Makefile.xmatchview | 28 ++++++++++++++++++++--------
 2 files changed, 21 insertions(+), 8 deletions(-)

diffs:
diff --git a/xmatchview/Makefile b/xmatchview/Makefile
index 838a4f6eac..e66e0502bd 100644
--- a/xmatchview/Makefile
+++ b/xmatchview/Makefile
@@ -53,6 +53,7 @@ do-install:
 	cd ${WRKSRC}/tarballs/fonts && ${PAX} -rw * ${DESTDIR}${PREFIX}/share/fonts/xmatchview 
 	cd ${WRKSRC}/test \
 	&& ${RM} -f xmv-FTL1_pa.fa_vs_FTL1_ss.fa.rep_m10_b10_r1_c2.png \
+	&& ${RM} -f xmv-FTL1_paMF.fa_vs_FTL1_ssMF.fa.paf_m80_b10_r1_c2.png \
 	&& ${PAX} -rw * ${DESTDIR}${PREFIX}/share/examples/xmatchview/xmatchview
 	cd ${WRKSRC}/test-hive \
 	&& ${RM} -f xmv-hive_i0_b1_c30_a0.75.svg \
diff --git a/xmatchview/files/Makefile.xmatchview b/xmatchview/files/Makefile.xmatchview
index e153b0d4a0..f90b6b778d 100644
--- a/xmatchview/files/Makefile.xmatchview
+++ b/xmatchview/files/Makefile.xmatchview
@@ -3,21 +3,33 @@
 XMATCHVIEW?=		xmatchview.py
 XMATCHVIEW_FONTDIR?=	@PREFIX@/share/fonts/xmatchview
 
-XMATCHVIEW_ARGS+=	-x FTL1_pa.fa_vs_FTL1_ss.fa.rep
-XMATCHVIEW_ARGS+=	-s FTL1_ss.fa
-XMATCHVIEW_ARGS+=	-q FTL1_pa.fa
+XMATCHVIEW_ARGS.rep+=	-x FTL1_pa.fa_vs_FTL1_ss.fa.rep
+XMATCHVIEW_ARGS.rep+=	-s FTL1_ss.fa
+XMATCHVIEW_ARGS.rep+=	-q FTL1_pa.fa
+XMATCHVIEW_ARGS.rep+=	-m 10
+XMATCHVIEW_ARGS.rep+=	-y FTL1_pa.gff
+XMATCHVIEW_ARGS.rep+=	-e FTL1_ss.gff
+CLEANFILES.rep+=	xmv-FTL1_pa.fa_vs_FTL1_ss.fa.rep_m10_b10_r1_c2.png
+
+XMATCHVIEW_ARGS.paf+=	-x FTL1_paMF.fa_vs_FTL1_ssMF.fa.paf
+XMATCHVIEW_ARGS.paf+=	-s FTL1_ssMF.fa
+XMATCHVIEW_ARGS.paf+=	-q FTL1_paMF.fa
+XMATCHVIEW_ARGS.paf+=	-m 80
+CLEANFILES.paf+=	xmv-FTL1_paMF.fa_vs_FTL1_ssMF.fa.paf_m80_b10_r1_c2.png
+
 XMATCHVIEW_ARGS+=	-a 200
-XMATCHVIEW_ARGS+=	-m 10
 XMATCHVIEW_ARGS+=	-b 10
 XMATCHVIEW_ARGS+=	-r 1
 XMATCHVIEW_ARGS+=	-c 2
 XMATCHVIEW_ARGS+=	-f png
-XMATCHVIEW_ARGS+=	-y FTL1_pa.gff
-XMATCHVIEW_ARGS+=	-e FTL1_ss.gff
 XMATCHVIEW_ARGS+=	-p ${XMATCHVIEW_FONTDIR}
 
 all:
-	${XMATCHVIEW} ${XMATCHVIEW_ARGS}
+.for f in rep paf
+	${XMATCHVIEW} ${XMATCHVIEW_ARGS} ${XMATCHVIEW_ARGS.${f}}
+.endfor
 
 clean:
-	rm -f xmv-FTL1_pa.fa_vs_FTL1_ss.fa.rep_m10_b10_r1_c2.png
+.for f in rep paf
+	rm -f ${CLEANFILES.${f}}
+.endfor