[med-svn] [Git][med-team/last-align][upstream] New upstream version 1652

[Charles Plessy (@plessy)]

Charles Plessy pushed to branch upstream at Debian Med / last-align


Commits:
2f174580 by Charles Plessy at 2026-07-10T12:06:21+09:00
New upstream version 1652
- - - - -


4 changed files:

- bin/maf-convert
- src/makefile
- test/maf-convert-test.out
- test/maf-convert-test.sh


Changes:

=====================================
bin/maf-convert
=====================================
@@ -1076,11 +1076,20 @@ def writeBlastTab(opts, formatName, geneticCode, maf):
            gapOpens, begB, endB, begA, endA]
 
     score, evalue = scoreAndEvalue(aLine)
+
+    bitScore = None
+    if score and opts.bitScoreA is not None and opts.bitScoreB is not None:
+        bitScore = opts.bitScoreA * float(score) - opts.bitScoreB
+        bitScore = "%.3g" % bitScore
+
+    if formatName == "blasttab+":
+        if not evalue: evalue = 'NA'
+        if not bitScore: bitScore = 'NA'
+
     if evalue:
         out.append(evalue)
-        if score and opts.bitScoreA is not None and opts.bitScoreB is not None:
-            bitScore = opts.bitScoreA * float(score) - opts.bitScoreB
-            out.append("%.3g" % bitScore)
+        if bitScore:
+            out.append(bitScore)
             if formatName == "blasttab+":
                 out += [seqLenB, seqLenA, score]
 


=====================================
src/makefile
=====================================
@@ -95,7 +95,7 @@ ScoreMatrixData.hh: ../data/*.mat
 	../build/mat-inc.sh ../data/*.mat > $@
 
 VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 1651) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1652) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
 
 VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
 


=====================================
test/maf-convert-test.out
=====================================
@@ -8349,6 +8349,9 @@ chrUn_KI270748v1	UN-L1PA2_pol#LINE/L1	93.39	227	15	0	3860	4540	1049	1275	1.5e-16
 chrUn_KI270748v1	UN-L1MA6_pol#LINE/L1	62.18	386	107	14	3661	2577	518	879	2.5e-152	546	93321	1275	1607.4
 chrUn_KI270748v1	UN-L1MA6_pol#LINE/L1	61.64	292	89	8	90089	89272	884	1164	2e-147	530	93321	1275	1559.7
 chrUn_KI270748v1	UN-L1PA16_pol#LINE/L1	64.07	359	96	11	17572	18588	527	864	3.8e-142	512	93321	1276	1508.0
+90089	chrX	92.38	656	8	21	49	670	23075590	23076237	NA	NA	2478	156040895	3061
+90089	chr7	87.72	114	1	6	776	676	121351143	121351256	NA	NA	2478	159345973	493
+90089	chr7	96.82	1699	8	33	2431	777	121348854	121350550	NA	NA	2478	159345973	9115
 UN-L1MA6_pol#LINE/L1	chrUn_KI270748v1	63.82	633	194	13	658	1273	13905	15715	0	1.08e+03
 UN-L1PA2_pol#LINE/L1	chrUn_KI270748v1	93.39	227	15	0	1049	1275	3860	4540	1.5e-169	603
 UN-L1MA6_pol#LINE/L1	chrUn_KI270748v1	62.18	386	107	14	518	879	3661	2577	2.5e-152	546


=====================================
test/maf-convert-test.sh
=====================================
@@ -25,6 +25,7 @@ maf2=bs100.maf
     $r -l120 blast HERVS71A.maf  # test ambiguous N bases
     $r blasttab $maf2
     $r blasttab+ frameshift-new.maf
+    $r blasttab+ 90089.maf
     $r -s2 blasttab frameshift-new.maf
     maf-cut DF0000170.5:633-798 herv30.maf | $r blasttab  # gaps at edges
     maf-cut DF0000170.5:633-798 herv30.maf | $r -s2 blasttab  # gaps at edges



View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/2f174580f6dbf28108ae4a295b231ae032e8f9dd

-- 
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/2f174580f6dbf28108ae4a295b231ae032e8f9dd
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