`impg` does not complain when selected range is exceeding the actual sequence length
subwaystation opened this issue · comments
For example:
./target/debug/impg -p ~/Downloads/impg/LPA.fa.gz.paf -r "chm13#0#tig00000001:0-10000000" -P -x
chm13#0#tig00000001 311357 0 10000000 + chm13#0#tig00000001 311357 0 10000000 10000000 10000000 255 cg:Z:10000000=
HG02572#1#tig00000001 309189 4000 71000 + chm13#0#tig00000001 311357 3958 71333 66953 67399 255 cg:Z:307=1I32=1I100=1I82=2D76=1X74=1D135=1D182=1I155=1I203=1D57=1D265=1X50=1I78=1I103=1I67=1I1355=1I827=1D4289=1X670=1X1047=1X1546=1D1880=1X3898=1X2366=1X731=1X2628=1I6025=8I696=1X671=1D801=387D1010=1D541=1X172=2I432=1X923=1X3132=1X216=1X461=1X858=1X5106=1X5652=2D5935=1X196=1X1469=1X3211=3I1294=1X2061=1X2888=
HG02572#0#tig00000005 311357 4500 104500 + chm13#0#tig00000001 311357 4506 104526 99901 100047 255 cg:Z:4I90=1I189=1X3=1I161=1I133=1D282=1D266=1X230=1I66=1I776=1X2210=1X1537=1X2401=1X217=1X1047=1X1700=1X1642=1X83=1X3531=1X113=1D252=1X2366=1X731=1X735=1X748=1X1043=4I3217=1X1251=1X1655=2I696=1X671=1D1305=1X422=1X1011=1X4878=1X1320=1X8362=1X2394=4D3550=1X2384=1X196=1X1469=1X620=9D2X2580=3I139=1X499=1X581=1X1736=1X397=1X3183=3I213=1X345=1X558=1X1300=1X381=1X528=1X72=1I1363=1X1954=1X1529=1I1687=2I1471=1X522=6D41=10D9=1X164=1X1160=2X2=1I2=2X160=14D8=1X1944=1X527=1I27=1X1332=1X1405=1X127=1X1344=1X1539=1X285=1X2692=1X1469=1X89=1X1066=1X553=1X515=1X766=1X497=1X1406=1X45=1X1055=1X681=
HG002#1#tig00000005 274138 0 99500 + chm13#0#tig00000001 311357 5045 104928 99417 99910 255 cg:Z:321=1D266=1X230=1I66=1I1342=1I353=1D791=1I3987=1X670=1X353=1X693=1X1546=1D1880=1X491=1X2469=1X936=1X2366=1X731=1X1624=1X1003=1I6025=12I696=1X671=1D801=387D1010=1D541=1X4661=1X216=1X461=1X858=1X5106=1X5650=4D5935=1X196=1X1469=1X3211=3I1287=1X6=1X2061=1X3183=3I213=1X904=1X2211=1X3390=1X2231=1X2455=1X575=1X1=4I1213=1X153=4D138=10D8=1X122=1X2376=1X1403=1X1334=1X1472=1X152=1X1672=1X71=1X330=1X435=1X912=1X751=1X7=1X180=1X514=1X713=1X240=1X89=1X4854=1X1055=1X343=1X678=1X60=
HG01358#1#tig00000010 240282 500 135000 + chm13#0#tig00000001 311357 6325 140855 134457 134548 255 cg:Z:11226=1X15649=2D2570=1X997=1I5886=1I855=1X10757=4D18472=1X16228=1X4704=1X490=1X3148=1X612=1X6667=1X1161=1X278=2D19=1X5=1X18=38D281=2D7250=1X284=9I113=2X220=1X1536=1X1498=1X1469=1X3988=1X2560=2I1323=1X180=1X5316=1X552=3I247=2I7819=1X79=
NA19240#0#tig00000001 285146 0 88500 + chm13#0#tig00000001 311357 10346 98907 88441 88569 255 cg:Z:2511=1X217=1X1047=1X1700=1X1642=1X83=1X3645=1D252=1X2366=1X731=1X735=1X5009=1X3603=1X671=1D2740=1X4436=1X441=1X1320=1X1761=1X1792=1X4807=1X2386=12D217=1X3332=1X2384=1X196=1X1469=1X620=9D2X2580=3I1927=2D979=1X447=1X538=1X121=1I2523=3I213=1X543=1X360=1X1174=1X1036=1X71=1D1010=1X2307=1X1793=1X1429=1I1464=1X522=18D33=4D5=1X1326=5D32=2D134=14D8=1X2499=1X1332=1X1405=1X127=1X1344=1X599=1X939=1X285=1X2692=1X1469=1X89=1X973=
HG002#0#tig00000001 329347 19000 181000 + chm13#0#tig00000001 311357 24586 186984 161943 162420 255 cg:Z:699=1X118=1X808=1X864=2I1477=1X3026=1X1618=2D696=1X671=1D801=387D1011=2I6741=1X1475=1X1539=1X64=1X4464=1X242=1I2035=1D935=2D1245=1X254=1X4263=1X170=1X196=1X1469=1X6567=1X2536=1D1X1=1X643=3I213=1X904=1X2284=1I2655=1X1887=1X1998=1I1464=1X571=6D1162=1X204=4D132=1X1=14D8=1X2499=1X18399=2D89=2I7526=1X3840=6I31625=1X5625=1X6385=4I19917=1X3021=1X127=1X2779=
HG002#0#tig00000001 329347 176500 328500 + chm13#0#tig00000001 311357 176932 328974 151958 152067 255 cg:Z:1592=1X127=1X2401=1X5551=1X3174=1X7915=1X2886=4D26670=1X1028=1X28=14I120=1X13446=1X3100=2D120=1X17003=1X12888=1X2990=1I245=56D799=1X8001=1X13541=1D13264=1X9279=1I162=1D455=1D79=1I77=1I266=1I51=1I269=1I2262=1I437=1I16=1I463=1I1141=1D1X44=1D68=
HG00733#1#tig00000008 283680 135500 283500 + chm13#0#tig00000001 311357 177004 325055 147976 148062 255 cg:Z:801=1X3248=1X5551=1X8433=10I62=1X75=1X2518=1X2888=2D24257=1X584=1X1827=1X14624=1X3100=2D120=1X17003=1X12888=1X3235=56D4799=2D41904=1I59=
HG01358#0#tig00000002 337324 245000 335500 + chm13#0#tig00000001 311357 235337 325865 90454 90547 255 cg:Z:815=1X1133=1X623=1X1478=1X36=6I120=1X694=2D1640=1X956=1X623=1X1455=4D19=1X34=8D815=2I1508=1X1432=1X279=1X923=1X196=1X79=1X95=2X157=4I50=4D62=1X5483=2I2325=1X3220=2I13375=1X3263=28D264=1D17286=1X6604=1I4473=1X8715=1I7543=1I45=1X1476=1X411=1X242=1X125=1X382=
HG00733#0#tig00000001 295824 206500 256500 + chm13#0#tig00000001 311357 235339 285544 49962 50215 255 cg:Z:813=1X1477=1X1400=1X79=1X95=2X209=8D62=1X1438=1X955=1X956=1X623=1X1478=1X34=8D22=1X792=2I1680=1X2996=4I869=2D357=1X1150=1X1712=1X1505=2D230=1X584=2D3221=1X923=1X1069=1X685=1X2953=1X1846=1X3739=1X3661=1X1078=1I1082=1X860=193D3406=1I1491=2I514=1X1918=
HG02572#1#tig00000001 309189 268500 286000 + chm13#0#tig00000001 311357 285845 303345 17487 17502 255 cg:Z:18=1X151=1X6791=1X2189=1X844=1X2650=1X747=1X640=1X4=1X274=1X2282=2D1=1X170=2I726=
NA19239#1#tig00000006 236974 219000 235500 + chm13#0#tig00000001 311357 304703 321202 16484 16502 255 cg:Z:1344=1X1284=1X1041=1X182=1X46=1X59=1X287=1X16=1X847=1X94=1X680=1X3083=1X912=2I772=1D272=1D3014=1X885=1I1666=
NA19240#0#tig00000001 285146 272000 285146 + chm13#0#tig00000001 311357 310425 323568 13099 13169 255 cg:Z:1782=1X1098=1X352=1D545=1X311=1X74=4I218=1X5=1X273=1X541=4D3768=1X131=1I285=1X1135=1X596=7I347=1X15=1X6=1X1=1X1=1X254=1X2=2I122=1D35=10I18=1D39=1D196=1D34=1D2=1X68=1D19=1D169=1D126=1D155=2I9=1D107=1D2=1X54=1D18=1D59=1D21=1D1X14=1D15=1D41=1D33=1X1=1X2=
NA19239#0#tig00000002 264003 259000 264003 + chm13#0#tig00000001 311357 324948 329959 4978 5031 255 cg:Z:2I14=1D84=1I19=1D67=1D191=2D367=1D353=1I21=1X4=1D83=1I113=1I119=1D18=1D151=1D248=1X31=1I82=1D90=1X69=1I39=1D41=1I26=1D109=2D191=2I118=1D302=1D114=1D243=1I259=1D6=1X207=2D107=1D1X44=1D257=1I36=1I27=1D82=1I34=1D194=1I9=1I183=1D51=1D104=1D45=1I26=2I
HG002#1#tig00000005 274138 272000 274138 + chm13#0#tig00000001 311357 327707 329838 2121 2146 255 cg:Z:15I638=1D320=1D168=1D21=1D2=1X42=1D134=1X185=1D115=1D438=1D58=
The result clearly is wrong.