# HG changeset patch
# User iuc
# Date 1637316555 0
# Node ID dd0cd2319ae5157cd2efd21740ac740debb31b8c
# Parent  37b5e1f0b5446d5762ec6a5d346a7df5526313f3
"planemo upload for repository https://github.com/ogotoh/spaln commit c06dea51e720899c3245d203c3a0abc9f179583f"

diff -r 37b5e1f0b544 -r dd0cd2319ae5 list_spaln_tables.xml
--- a/list_spaln_tables.xml	Thu Jul 16 07:57:10 2020 -0400
+++ b/list_spaln_tables.xml	Fri Nov 19 10:09:15 2021 +0000
@@ -78,7 +78,7 @@
             <output name="output">
                 <assert_contents>
                     <has_line_matching expression="5\t4\tActinopteri\tcynosemi\tFish_mdl\tCynoglossus semilaevis" />
-                    <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tMagnolio\tZea mays" />
+                    <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tAngiosp\tZea mays" />
                 </assert_contents>
             </output>
         </test>
@@ -94,7 +94,7 @@
             <output name="output">
                 <assert_contents>
                     <has_line_matching expression="5\t4\tActinopteri\tcynosemi\tFish_mdl\tCynoglossus semilaevis" />
-                    <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tMagnolio\tZea mays" />
+                    <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tAngiosp\tZea mays" />
                 </assert_contents>
             </output>
         </test>
diff -r 37b5e1f0b544 -r dd0cd2319ae5 macros.xml
--- a/macros.xml	Thu Jul 16 07:57:10 2020 -0400
+++ b/macros.xml	Fri Nov 19 10:09:15 2021 +0000
@@ -1,3 +1,3 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.4.03</token>
+    <token name="@TOOL_VERSION@">2.4.6</token>
 </macros>
\ No newline at end of file
diff -r 37b5e1f0b544 -r dd0cd2319ae5 spaln.xml
--- a/spaln.xml	Thu Jul 16 07:57:10 2020 -0400
+++ b/spaln.xml	Fri Nov 19 10:09:15 2021 +0000
@@ -38,6 +38,8 @@
             #if str($adv.max_gene_length).strip() != ''
                 -XG'${adv.max_gene_length}'
             #end if
+            $adv.format_remote_queries
+            $adv.salvage_mode
         #end if
         '$genome' '$query' >'$output1' 
     ]]></command>
@@ -90,6 +92,8 @@
             <param argument="-yL" name="min_intron_len" type="integer" value="30" label="Minimum expected length of intron" />
             <param argument="-yZ" name="intron_potential_weight" type="integer" value="0" label="Weight for intron potential" />
             <param argument="-XG" name="max_gene_length" type="text" label="Reset maximum expected gene size, suffix k or M is effective" />
+            <param argument="-yX" name="format_remote_queries" type="boolean" checked="false" truevalue="-yX" falsevalue="" label="Format for remote queries" help="More sensitive but less economic than the default" />
+            <param argument="-XS" name="salvage_mode" type="boolean" checked="false" truevalue="-XS" falsevalue="" label="Activate salvage mode" help="Examine all positively scored blocks. Considerably slow." />
         </when>
     </conditional>
     </inputs>
diff -r 37b5e1f0b544 -r dd0cd2319ae5 test-data/output1.bed12
--- a/test-data/output1.bed12	Thu Jul 16 07:57:10 2020 -0400
+++ b/test-data/output1.bed12	Fri Nov 19 10:09:15 2021 +0000
@@ -1,2 +1,2 @@
 track name=Spaln description="NP_001121846.1" useScore=1
-scaffold_1	16	10418	NP_001121846.1	530	+	16	10418	255,0,0	16	46,33,122,127,33,4,127,33,6,18,15,11,13,24,24,24,	0,111,401,7107,7546,7642,7721,7908,8278,8849,8963,9050,9959,10028,10212,10378
+scaffold_1	16	10418	NP_001121846.1	355	+	16	10418	255,0,0	16	46,30,122,127,33,4,127,33,6,18,15,11,13,24,24,24,	0,288,401,7107,7546,7642,7721,7908,8278,8849,8963,9050,9959,10028,10212,10378
diff -r 37b5e1f0b544 -r dd0cd2319ae5 test-data/output1.tabular
--- a/test-data/output1.tabular	Thu Jul 16 07:57:10 2020 -0400
+++ b/test-data/output1.tabular	Fri Nov 19 10:09:15 2021 +0000
@@ -1,18 +1,18 @@
 # rID	  gID	   %id	  ExonL	 MisMch	 Unpair	 ref_l	  ref_r	  tgt_l	  tgt_r	 eScore	 IntrnL	 iScore	 Sig3/I	 Sig5/T  # -  X P DiNuc
-NP_001121846.1	scaffold_1	  21.43	     46	     11	      0	      1	     14	     17	     62	   79.7	      0	    0.0	  66.40	   0.90  0 0  0 0   .  
-NP_001121846.1	scaffold_1	  12.50	     33	      8	      3	     15	     27	    128	    160	   -4.3	     65	  -23.9	  -5.20	  10.70  0 0  0 1 GT.AG
-NP_001121846.1	scaffold_1	  68.29	    122	     13	      0	     28	     68	    418	    539	  210.5	    257	   -0.1	  16.10	   6.60  0 0  0 1 GT.AG
-NP_001121846.1	scaffold_1	  64.29	    127	     15	      0	     69	    110	   7124	   7250	  187.0	   6584	  -24.3	  14.60	  17.80  0 0  0 0 GT.AG
-NP_001121846.1	scaffold_1	   9.09	     33	     10	      0	    111	    121	   7563	   7595	   11.0	    312	   -4.2	   5.70	   5.20  0 0  0 1 GT.AG
-NP_001121846.1	scaffold_1	   0.00	      4	      2	      0	    122	    123	   7659	   7662	   21.2	     63	   -6.4	   7.90	  13.90  0 0  0 1 GT.AG
-NP_001121846.1	scaffold_1	  20.45	    127	     31	      2	    124	    165	   7738	   7864	   21.7	     75	    5.0	  11.80	  13.20  0 0  0 2 GT.AG
-NP_001121846.1	scaffold_1	   9.09	     33	     10	      0	    166	    176	   7925	   7957	   26.1	     60	    1.0	   7.20	   9.70  0 0  0 0 GT.AG
-NP_001121846.1	scaffold_1	  50.00	      6	      1	      0	    177	    178	   8295	   8300	   29.4	    337	   -9.5	   8.90	  10.80  0 0  0 0 GT.AG
-NP_001121846.1	scaffold_1	  16.67	     18	      5	      0	    179	    184	   8866	   8883	   31.0	    565	   -7.7	  12.00	  17.60  0 0  0 0 GT.AG
-NP_001121846.1	scaffold_1	   0.00	     15	      5	      0	    185	    189	   8980	   8994	   30.3	     96	   11.1	  15.90	   9.10  0 0  0 0 GT.AG
-NP_001121846.1	scaffold_1	   0.00	     11	      4	      0	    190	    193	   9067	   9077	   27.0	     72	   -4.0	   7.10	   7.60  0 0  0 0 GT.AG
-NP_001121846.1	scaffold_1	  25.00	     13	      3	      0	    194	    197	   9976	   9988	   28.5	    898	  -22.1	   6.80	  15.40  0 0  0 2 GT.AG
-NP_001121846.1	scaffold_1	  37.50	     24	      5	      0	    198	    205	  10045	  10068	   27.5	     56	    3.7	   7.70	   5.10  0 0  0 0 GT.AG
-NP_001121846.1	scaffold_1	  25.00	     24	      6	      0	    206	    213	  10229	  10252	   38.3	    160	   -6.9	  13.10	  12.60  0 0  0 0 GT.AG
-NP_001121846.1	scaffold_1	  20.00	     24	      6	      1	    214	    222	  10395	  10418	   23.3	    142	    0.3	  12.40	  12.60  0 0  0 0 GT.AG
-@ scaffold_1 + ( 17 10418 ) NP_001121846.1 222 ( 1 222 ) S: 627.0 =: 36.5 C: 97.3 T#: 135 T-: 6 B#: 0 B-: 0 X: 0 Nexn: 16
+NP_001121846.1	scaffold_1	  23.53	     46	     10	      2	      1	     15	     17	     62	    7.1	      0	    0.0	   6.64	   0.09  0 0  0 0   .  
+NP_001121846.1	scaffold_1	  14.29	     30	      8	      2	     16	     27	    305	    334	    0.6	    242	   -1.6	   0.99	   0.40  0 0  0 1 GT.AG
+NP_001121846.1	scaffold_1	  65.85	    122	     14	      0	     28	     68	    418	    539	   20.7	     83	   -0.1	   1.61	   0.65  0 0  0 1 GT.AG
+NP_001121846.1	scaffold_1	  64.29	    127	     15	      0	     69	    110	   7124	   7250	   18.7	   6584	   -2.5	   1.45	   1.77  0 0  0 0 GT.AG
+NP_001121846.1	scaffold_1	   9.09	     33	     10	      0	    111	    121	   7563	   7595	    1.1	    312	   -0.4	   0.56	   0.51  0 0  0 1 GT.AG
+NP_001121846.1	scaffold_1	   0.00	      4	      2	      0	    122	    123	   7659	   7662	    2.1	     63	   -0.7	   0.78	   1.38  0 0  0 1 GT.AG
+NP_001121846.1	scaffold_1	  20.00	    127	     31	      3	    124	    165	   7738	   7864	    2.2	     75	    0.5	   1.17	   1.32  0 0  0 2 GT.AG
+NP_001121846.1	scaffold_1	   9.09	     33	     10	      0	    166	    176	   7925	   7957	    2.6	     60	    0.1	   0.71	   0.96  0 0  0 0 GT.AG
+NP_001121846.1	scaffold_1	  50.00	      6	      1	      0	    177	    178	   8295	   8300	    2.9	    337	   -1.0	   0.88	   1.07  0 0  0 0 GT.AG
+NP_001121846.1	scaffold_1	  16.67	     18	      5	      0	    179	    184	   8866	   8883	    3.1	    565	   -0.8	   1.20	   1.75  0 0  0 0 GT.AG
+NP_001121846.1	scaffold_1	   0.00	     15	      5	      0	    185	    189	   8980	   8994	    3.0	     96	    1.1	   1.58	   0.90  0 0  0 0 GT.AG
+NP_001121846.1	scaffold_1	   0.00	     11	      4	      0	    190	    193	   9067	   9077	    2.7	     72	   -0.4	   0.70	   0.75  0 0  0 0 GT.AG
+NP_001121846.1	scaffold_1	  25.00	     13	      3	      0	    194	    197	   9976	   9988	    2.8	    898	   -2.2	   0.67	   1.54  0 0  0 2 GT.AG
+NP_001121846.1	scaffold_1	  37.50	     24	      5	      0	    198	    205	  10045	  10068	    2.8	     56	    0.4	   0.77	   0.51  0 0  0 0 GT.AG
+NP_001121846.1	scaffold_1	  25.00	     24	      6	      0	    206	    213	  10229	  10252	    3.8	    160	   -0.7	   1.30	   1.25  0 0  0 0 GT.AG
+NP_001121846.1	scaffold_1	  20.00	     24	      6	      1	    214	    222	  10395	  10418	    4.6	    142	    0.0	   1.24	   3.54  0 0  0 0 GT.AG
+@ scaffold_1 + ( 17 10418 ) NP_001121846.1 [1:222] ( 1 222 ) S: 420.1 =: 36.5 C: 97.3 T#: 135 T-: 8 B#: 0 B-: 0 X: 0 Nexn: 16 HC:  0.0
diff -r 37b5e1f0b544 -r dd0cd2319ae5 test-data/output1_gff_genes.gff3
--- a/test-data/output1_gff_genes.gff3	Thu Jul 16 07:57:10 2020 -0400
+++ b/test-data/output1_gff_genes.gff3	Fri Nov 19 10:09:15 2021 +0000
@@ -1,20 +1,20 @@
 ##gff-version	3
 ##sequence-region	scaffold_1 1 59940
-scaffold_1	ALN	gene	17	10418	627	+	.	ID=gene00001;Name=scaffold_1_5
-scaffold_1	ALN	mRNA	17	10418	627	+	.	ID=mRNA00001;Parent=gene00001;Name=scaffold_1_5
-scaffold_1	ALN	cds	17	62	79	+	0	ID=cds00001;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 1 14 +
-scaffold_1	ALN	cds	128	160	-4	+	2	ID=cds00002;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 15 27 +
-scaffold_1	ALN	cds	418	539	210	+	2	ID=cds00003;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 28 68 +
-scaffold_1	ALN	cds	7124	7250	187	+	0	ID=cds00004;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 69 110 +
-scaffold_1	ALN	cds	7563	7595	11	+	2	ID=cds00005;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 111 121 +
+scaffold_1	ALN	gene	17	10418	420	+	.	ID=gene00001;Name=scaffold_1_5
+scaffold_1	ALN	mRNA	17	10418	420	+	.	ID=mRNA00001;Parent=gene00001;Name=scaffold_1_5
+scaffold_1	ALN	cds	17	62	71	+	0	ID=cds00001;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 1 15 +
+scaffold_1	ALN	cds	305	334	5	+	2	ID=cds00002;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 16 27 +
+scaffold_1	ALN	cds	418	539	207	+	2	ID=cds00003;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 28 68 +
+scaffold_1	ALN	cds	7124	7250	186	+	0	ID=cds00004;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 69 110 +
+scaffold_1	ALN	cds	7563	7595	10	+	2	ID=cds00005;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 111 121 +
 scaffold_1	ALN	cds	7659	7662	21	+	2	ID=cds00006;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 122 123 +
 scaffold_1	ALN	cds	7738	7864	21	+	1	ID=cds00007;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 124 165 +
-scaffold_1	ALN	cds	7925	7957	26	+	0	ID=cds00008;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 166 176 +
+scaffold_1	ALN	cds	7925	7957	25	+	0	ID=cds00008;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 166 176 +
 scaffold_1	ALN	cds	8295	8300	29	+	0	ID=cds00009;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 177 178 +
-scaffold_1	ALN	cds	8866	8883	31	+	0	ID=cds00010;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 179 184 +
+scaffold_1	ALN	cds	8866	8883	30	+	0	ID=cds00010;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 179 184 +
 scaffold_1	ALN	cds	8980	8994	30	+	0	ID=cds00011;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 185 189 +
-scaffold_1	ALN	cds	9067	9077	27	+	0	ID=cds00012;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 190 193 +
+scaffold_1	ALN	cds	9067	9077	26	+	0	ID=cds00012;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 190 193 +
 scaffold_1	ALN	cds	9976	9988	28	+	1	ID=cds00013;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 194 197 +
 scaffold_1	ALN	cds	10045	10068	27	+	0	ID=cds00014;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 198 205 +
 scaffold_1	ALN	cds	10229	10252	38	+	0	ID=cds00015;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 206 213 +
-scaffold_1	ALN	cds	10395	10418	23	+	0	ID=cds00016;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +
+scaffold_1	ALN	cds	10395	10418	46	+	0	ID=cds00016;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +
diff -r 37b5e1f0b544 -r dd0cd2319ae5 test-data/output1_gff_matches.gff3
--- a/test-data/output1_gff_matches.gff3	Thu Jul 16 07:57:10 2020 -0400
+++ b/test-data/output1_gff_matches.gff3	Fri Nov 19 10:09:15 2021 +0000
@@ -1,18 +1,18 @@
 ##gff-version	3
 ##sequence-region	scaffold_1 1 59940
-scaffold_1	ALN	nucleotide_to_protein_match	17	62	79	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 1 14 +;Gap=D1 M14 
-scaffold_1	ALN	nucleotide_to_protein_match	128	160	-4	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 15 27 +;Gap=M5 I3 M1 D1 M4 
-scaffold_1	ALN	nucleotide_to_protein_match	418	539	210	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 28 68 +;Gap=M41 
-scaffold_1	ALN	nucleotide_to_protein_match	7124	7250	187	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 69 110 +;Gap=M42 
-scaffold_1	ALN	nucleotide_to_protein_match	7563	7595	11	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 111 121 +;Gap=M11 
+scaffold_1	ALN	nucleotide_to_protein_match	17	62	71	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 1 15 +;Gap=D1 M13 I1 M1 
+scaffold_1	ALN	nucleotide_to_protein_match	305	334	5	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 16 27 +;Gap=M6 I2 M4 
+scaffold_1	ALN	nucleotide_to_protein_match	418	539	207	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 28 68 +;Gap=M41 
+scaffold_1	ALN	nucleotide_to_protein_match	7124	7250	186	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 69 110 +;Gap=M42 
+scaffold_1	ALN	nucleotide_to_protein_match	7563	7595	10	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 111 121 +;Gap=M11 
 scaffold_1	ALN	nucleotide_to_protein_match	7659	7662	21	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 122 123 +;Gap=M2 
 scaffold_1	ALN	nucleotide_to_protein_match	7738	7864	21	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 124 165 +;Gap=M14 D1 M7 I2 M19 D1 
-scaffold_1	ALN	nucleotide_to_protein_match	7925	7957	26	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 166 176 +;Gap=M11 
+scaffold_1	ALN	nucleotide_to_protein_match	7925	7957	25	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 166 176 +;Gap=M11 
 scaffold_1	ALN	nucleotide_to_protein_match	8295	8300	29	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 177 178 +;Gap=M2 
-scaffold_1	ALN	nucleotide_to_protein_match	8866	8883	31	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 179 184 +;Gap=M6 
+scaffold_1	ALN	nucleotide_to_protein_match	8866	8883	30	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 179 184 +;Gap=M6 
 scaffold_1	ALN	nucleotide_to_protein_match	8980	8994	30	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 185 189 +;Gap=M5 
-scaffold_1	ALN	nucleotide_to_protein_match	9067	9077	27	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 190 193 +;Gap=M4 
+scaffold_1	ALN	nucleotide_to_protein_match	9067	9077	26	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 190 193 +;Gap=M4 
 scaffold_1	ALN	nucleotide_to_protein_match	9976	9988	28	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 194 197 +;Gap=M4 
 scaffold_1	ALN	nucleotide_to_protein_match	10045	10068	27	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 198 205 +;Gap=M8 
 scaffold_1	ALN	nucleotide_to_protein_match	10229	10252	38	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 206 213 +;Gap=M8 
-scaffold_1	ALN	nucleotide_to_protein_match	10395	10418	23	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +;Gap=M5 I1 M3 
+scaffold_1	ALN	nucleotide_to_protein_match	10395	10418	46	+	.	ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +;Gap=M5 I1 M3 
diff -r 37b5e1f0b544 -r dd0cd2319ae5 test-data/output2.tabular
--- a/test-data/output2.tabular	Thu Jul 16 07:57:10 2020 -0400
+++ b/test-data/output2.tabular	Fri Nov 19 10:09:15 2021 +0000
@@ -1,7 +1,7 @@
 # rID	  gID	   %id	  ExonL	 MisMch	 Unpair	 ref_l	  ref_r	  tgt_l	  tgt_r	 eScore	 IntrnL	 iScore	 Sig3/I	 Sig5/T  # -  X P DiNuc
-NP_001121846.1	scaffold_1	  11.11	     91	     24	      0	      1	     27	     17	    107	   54.8	      0	    0.0	  66.40	   5.40  0 0  0 0   .  
-NP_001121846.1	scaffold_1	  65.85	    122	     14	      0	     28	     68	    418	    539	  210.7	    310	  -20.3	  17.40	   8.60  0 0  0 1 GT.AG
-NP_001121846.1	scaffold_1	  64.29	    127	     15	      0	     69	    110	   7124	   7250	  188.0	   6584	  -33.9	  16.50	  16.90  0 0  0 0 GT.AG
-NP_001121846.1	scaffold_1	  28.57	    147	     30	      0	    111	    152	  44187	  44333	   28.7	  36936	  -44.6	  10.00	   9.60  0 0  0 1 GT.AG
-NP_001121846.1	scaffold_1	  20.55	    221	     52	      3	    153	    222	  44595	  44815	   23.4	    261	  -18.9	  14.00	   9.60  0 0  0 1 GT.AG
-@ scaffold_1 + ( 17 44815 ) NP_001121846.1 222 ( 1 222 ) S: 349.5 =: 37.8 C: 98.6 T#: 135 T-: 3 B#: 0 B-: 0 X: 0 Nexn: 5
+NP_001121846.1	scaffold_1	  10.00	     91	     24	      3	      1	     27	     17	    107	    5.5	      0	    0.0	   6.64	   0.58  0 0  0 0   .  
+NP_001121846.1	scaffold_1	  65.85	    122	     14	      0	     28	     68	    418	    539	   21.2	    310	   -1.7	   1.88	   0.83  0 0  0 1 GT.AG
+NP_001121846.1	scaffold_1	  64.29	    127	     15	      0	     69	    110	   7124	   7250	   18.9	   6584	   -3.1	   1.77	   1.71  0 0  0 0 GT.AG
+NP_001121846.1	scaffold_1	  24.49	    147	     30	      7	    111	    152	  44187	  44333	    3.0	  36936	   -4.2	   1.03	   1.02  0 0  0 1 GT.AG
+NP_001121846.1	scaffold_1	  18.75	    221	     52	     10	    153	    222	  44595	  44815	    4.8	    261	   -1.6	   1.50	   3.36  0 0  0 1 GT.AG
+@ scaffold_1 + ( 17 44815 ) NP_001121846.1 [1:222] ( 1 222 ) S: 324.7 =: 37.8 C: 98.6 T#: 135 T-: 20 B#: 0 B-: 0 X: 0 Nexn: 5 HC:  0.0