02336754147822f5aa61ba13277123b2cc629001
markd
  Thu May 20 08:38:55 2021 -0700
Moved pslMap, pslMapPostChain, pslRc, pslSwap to src/utils, as they do not have hg/lib dependencies.

diff --git src/utils/pslMap/tests/input/gapBothProtMRna.blast src/utils/pslMap/tests/input/gapBothProtMRna.blast
new file mode 100644
index 0000000..b65f045
--- /dev/null
+++ src/utils/pslMap/tests/input/gapBothProtMRna.blast
@@ -0,0 +1,218 @@
+TBLASTN 2.2.6 [Apr-09-2003]
+
+
+Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
+Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
+"Gapped BLAST and PSI-BLAST: a new generation of protein database search
+programs",  Nucleic Acids Res. 25:3389-3402.
+
+Query= O14492
+         (632 letters)
+
+Database: /cluster/bluearc/markd/snpProtein/kgMrna.fa 
+           37,452 sequences; 89,350,383 total letters
+
+Searching..................................................done
+
+                                                                 Score    E
+Sequences producing significant alignments:                      (bits) Value
+
+AB000520                                                              966   0.0  
+AB037720                                                              310   4e-84
+AL713760                                                              310   4e-84
+
+>AB000520
+          Length = 2110
+
+ Score =  966 bits (2498), Expect = 0.0
+ Identities = 489/611 (80%), Positives = 489/611 (80%)
+ Frame = +2
+
+Query: 22  DWRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL 81
+           DWRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL
+Sbjct: 191 DWRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL 370
+
+Query: 82  VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDVSTHAATKARVRKGFSLRNMS 141
+           VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDVSTHAATKARVRKGFSLRNMS
+Sbjct: 371 VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDVSTHAATKARVRKGFSLRNMS 550
+
+Query: 142 LCVVDGVRDMWHRRASPEPDAAAAPRTAEPRDKWXXXXXXXXXXAAKVELVDIQREGALR 201
+           LCVVDGVRDMWHRRASPEPDAAAAPRTAEPRDKW          AAKVELVDIQREGALR
+Sbjct: 551 LCVVDGVRDMWHRRASPEPDAAAAPRTAEPRDKWTRRLRLSRTLAAKVELVDIQREGALR 730
+
+Query: 202 FMVXXXXXXXXXXXXQWQKCXXXXXXXXXXXXXXXXXXXPPKASRPKVSIPLSAIIEVRT 261
+           FMV            QWQKC                   PPKASRPKVSIPLSAIIEVRT
+Sbjct: 731 FMVADDAAAGSGGSAQWQKCRLLLRRAVAEERFRLEFFVPPKASRPKVSIPLSAIIEVRT 910
+
+Query: 262 TMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGDSEEDTELSCTRG 321
+           TMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGDSEEDTELSCTRG
+Sbjct: 911 TMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGDSEEDTELSCTRG 1090
+
+Query: 322 GCLASRVASCSCELLTDAVDLPRPPETTAVGAVVTAPHSRGRDAVRESLIHVPLETFLQT 381
+           GCLASRVASCSCELLTDAVDLPRPPETTAVGAVVTAPHSRGRDAVRESLIHVPLETFLQT
+Sbjct: 1091GCLASRVASCSCELLTDAVDLPRPPETTAVGAVVTAPHSRGRDAVRESLIHVPLETFLQT 1270
+
+Query: 382 LESPGGSGSDSNNTGEQGAETDPEAEPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGL 441
+           LESPGGSGSDSNNTGEQGAETDPEAEPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGL
+Sbjct: 1271LESPGGSGSDSNNTGEQGAETDPEAEPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGL 1450
+
+Query: 442 FVIRQSETRPGEYVLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPL 501
+           FVIRQSETRPGEYVLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPL
+Sbjct: 1451FVIRQSETRPGEYVLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPL 1630
+
+Query: 502 ESGGSADITLRSYVRAQDXXXXXXXXXXXXXXXXXCWSDSPGQHYFXXXXXXXXXXXXXX 561
+           ESGGSADITLRSYVRAQD                 CWSDSPGQHYF              
+Sbjct: 1631ESGGSADITLRSYVRAQDPPPEPGPTPPAAPASPACWSDSPGQHYFSSLAAAACPPASPS 1810
+
+Query: 562 XXXXXXXXXXXXXXXXXXXXXXRPVEGQLSARSRSNSXXXXXXXXXXXXXXXXXXXXXXX 621
+                                 RPVEGQLSARSRSNS                       
+Sbjct: 1811DAAGASSSSASSSSAASGPAPPRPVEGQLSARSRSNSAERLLEAVAATAAEEPPEAAPGR 1990
+
+Query: 622 XXXXXNQYSFY 632
+                NQYSFY
+Sbjct: 1991ARAVENQYSFY 2023
+
+
+>AB037720
+          Length = 6043
+
+ Score =  310 bits (795), Expect = 4e-84
+ Identities = 223/601 (37%), Positives = 288/601 (47%), Gaps = 108/601 (17%)
+ Frame = +1
+
+Query: 23   WRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL- 81
+            WR+FCE HA+AAA+DFA +F  +L  +P Y  P A A+FSR FA  FL  F  EV R   
+Sbjct: 3367 WREFCESHARAAALDFARRFRLYLASHPQYAGPGAEAAFSRRFAELFLQHFEAEVARASG 3546
+
+Query: 82   -----VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDV----------STHAA 126
+                 +  P + GA +S   +  E         A  G SRSSED+          S+  +
+Sbjct: 3547 SLSPPILAPLSPGAEISPHDLSLESCRVGG-PLAVLGPSRSSEDLAGPLPSSVSSSSTTS 3723
+
+Query: 127  TKARVRKGFSLRNMSLCVVDGVRDMWHRRASPEPDAAAAPRTAE---------------- 170
+            +K +++K FSLR++   V   VR +   R + +P ++A P                    
+Sbjct: 3724 SKPKLKKRFSLRSVGRSVRGSVRGILQWRGTVDPPSSAGPLETSSGPPVLGGNSNSNSSG 3903
+
+Query: 171  ---------------PRDKWXXXXXXXXXXAAKVELVD----IQREGALRFMVXXXXX-- 209
+                           P ++W               L D    +QRE  L FM        
+Sbjct: 3904 GAGTVGRGLVSDGTSPGERWTHRFERLRLSRGGGALKDGAGMVQREELLSFMGAEEAAPD 4083
+
+Query: 210  --------------XXXXXXXQWQKCXXXXXXXXXXXXXXXXXXX-PPKASRPKVSIPLS 254
+                                 QWQKC                    PPKASRP++SIP S
+Sbjct: 4084 PAGVGRGGGVAGPPSGGGGQPQWQKCRLLLRSEGEGGGGSRLEFFVPPKASRPRLSIPCS 4263
+
+Query: 255  AIIEVRTTMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGD----S 310
+            +I +VRTT  LEMP+++NTFV+KVE  +EYI+ET+D+    +WV+DIQ C+ PG     S
+Sbjct: 4264 SITDVRTTTALEMPDRENTFVVKVEGPSEYIMETVDAQHVKAWVSDIQECLSPGPCPATS 4443
+
+Query: 311  EEDTELSCTRGGCLASRVASCSCEL--LTDAVDLPR------PPETT------AVG---- 352
+                 L    G    +R  + S EL  L  +  LP       P E+       A G    
+Sbjct: 4444 PRPMTLPLAPGTSFLTRENTDSLELSCLNHSESLPSQDLLLGPSESNDRLSQGAYGGLSD 4623
+
+Query: 353  ----------AVVTAPHSRGRDAVRESLI-HVPLETFLQT-----LESPGGS-GSDSNNT 395
+                      A + A H    + +   L   +P+E    T     L +P     +    T
+Sbjct: 4624 RPSASISPSSASIAASHFDSMELLPPELPPRIPIEEGPPTGTVHPLSAPYPPLDTPETAT 4803
+
+Query: 396  GEQGAETDPEA-EPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGLFVIRQSETRPGEY 454
+            G    + +PE  E +  LS YPWFHG LSR+KAAQLVL GG  +HG+F++RQSETR GEY
+Sbjct: 4804 GSFLFQGEPEGGEGDQPLSGYPWFHGMLSRLKAAQLVLTGGTGSHGVFLVRQSETRRGEY 4983
+
+Query: 455  VLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPLESGGSADITLRSY 514
+            VLTFNFQGKAKHLRLSLN  GQC VQHLWFQS+ DML HF  HPIPLESGGS+D+ L SY
+Sbjct: 4984 VLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSY 5163
+
+Query: 515  V 515
+            V
+Sbjct: 5164 V 5166
+
+
+>AL713760
+          Length = 4876
+
+ Score =  310 bits (795), Expect = 4e-84
+ Identities = 222/601 (36%), Positives = 288/601 (47%), Gaps = 108/601 (17%)
+ Frame = +3
+
+Query: 23   WRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL- 81
+            WR+FCE HA+AAA+DFA +F  +L  +P Y  P A A+FSR FA  FL  F  EV R   
+Sbjct: 2178 WREFCESHARAAALDFARRFRLYLASHPQYAGPGAEAAFSRRFAELFLQHFEAEVARASG 2357
+
+Query: 82   -----VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDV----------STHAA 126
+                 +  P + GA +S   +  E         A  G SRSSED+          S+  +
+Sbjct: 2358 SLSPPILAPLSPGAEISPHDLSLESCRVGG-PLAVLGPSRSSEDLAGPLPSSVSSSSTTS 2534
+
+Query: 127  TKARVRKGFSLRNMSLCVVDGVRDMWHRRASPEPDAAAAPRTAE---------------- 170
+            +K +++K FSLR++   V   VR +   R + +P ++A P                    
+Sbjct: 2535 SKPKLKKRFSLRSVGRSVRGSVRGILQWRGTVDPPSSAGPLETSSGPPVLGGNSNSNSSG 2714
+
+Query: 171  ---------------PRDKWXXXXXXXXXXAAKVELVD----IQREGALRFMVXXXXX-- 209
+                           P ++W               L D    +QRE  L FM        
+Sbjct: 2715 GAGTVGRGLVSDGTSPGERWTHRFERLRLSRGGGALKDGAGMVQREELLSFMGAEEAAPD 2894
+
+Query: 210  --------------XXXXXXXQWQKCXXXXXXXXXXXXXXXXXXX-PPKASRPKVSIPLS 254
+                                 QWQKC                    PPKASRP++SIP S
+Sbjct: 2895 PAGVGRGGGVAGPPSGGGGQPQWQKCRLLLRSEGEGGGGSRLEFFVPPKASRPRLSIPCS 3074
+
+Query: 255  AIIEVRTTMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGD----S 310
+            +I +VRTT  LEMP+++NTFV+KVE  +EYI+ET+D+    +WV+DIQ C+ PG     S
+Sbjct: 3075 SITDVRTTTALEMPDRENTFVVKVEGPSEYIMETVDAQHVKAWVSDIQECLSPGPCPATS 3254
+
+Query: 311  EEDTELSCTRGGCLASRVASCSCEL--LTDAVDLPR------PPETT------AVG---- 352
+                 L    G    +R  + S EL  L  +  LP       P E+       A G    
+Sbjct: 3255 PRPMTLPLAPGTSFLTRENTDSLELSCLNHSESLPSQDLLLGPSESNDRLSQGAYGGLSD 3434
+
+Query: 353  ----------AVVTAPHSRGRDAVRESLI-HVPLET-----FLQTLESPGGS-GSDSNNT 395
+                      A + A H    + +   L   +P+E       +  L +P     +    T
+Sbjct: 3435 RPSASISPSSASIAASHFDSMELLPPELPPRIPIEEGPPAGTVHPLSAPYPPLDTPETAT 3614
+
+Query: 396  GEQGAETDPEA-EPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGLFVIRQSETRPGEY 454
+            G    + +PE  E +  LS YPWFHG LSR+KAAQLVL GG  +HG+F++RQSETR GEY
+Sbjct: 3615 GSFLFQGEPEGGEGDQPLSGYPWFHGMLSRLKAAQLVLTGGTGSHGVFLVRQSETRRGEY 3794
+
+Query: 455  VLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPLESGGSADITLRSY 514
+            VLTFNFQGKAKHLRLSLN  GQC VQHLWFQS+ DML HF  HPIPLESGGS+D+ L SY
+Sbjct: 3795 VLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSY 3974
+
+Query: 515  V 515
+            V
+Sbjct: 3975 V 3977
+
+
+  Database: /cluster/bluearc/markd/snpProtein/kgMrna.fa
+    Posted date:  Nov 13, 2003  9:35 AM
+  Number of letters in database: 89,350,383
+  Number of sequences in database:  37,452
+  
+Lambda     K      H
+   0.317    0.132    0.402 
+
+Gapped
+Lambda     K      H
+   0.267   0.0410    0.140 
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Hits to DB: 65,697,381
+Number of Sequences: 37452
+Number of extensions: 1123227
+Number of successful extensions: 8055
+Number of sequences better than 10.0: 84
+Number of HSP's better than 10.0 without gapping: 3446
+Number of HSP's successfully gapped in prelim test: 592
+Number of HSP's that attempted gapping in prelim test: 4353
+Number of HSP's gapped (non-prelim): 4528
+length of query: 632
+length of database: 29,783,461
+effective HSP length: 113
+effective length of query: 519
+effective length of database: 25,551,385
+effective search space: 13261168815
+effective search space used: 13261168815
+frameshift window, decay const: 50,  0.1
+T: 13
+A: 40
+X1: 16 ( 7.3 bits)
+X2: 38 (14.6 bits)
+X3: 64 (24.7 bits)
+S1: 41 (21.7 bits)
+S2: 67 (30.4 bits)